HEADER RIBONUCLEIC ACID 18-AUG-88 ARB005 TITLE THE STRUCTURE OF THE RIBODINUCLEOSIDE MONOPHOSPHATE TITLE 2 GUANYLYL-3',5'-CYTIDINE AS ITS AMMONIUM OCTAHYDRATE SALT COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (5'-R(*GP*C)-3'); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS A-RNA, DOUBLE HELIX EXPDTA X-RAY DIFFRACTION AUTHOR A.AGGARWAL,S.A.ISLAM,R.KURODA,M.R.SANDERSON,S.NEIDLE, AUTHOR 2 H.M.BERMAN REVDAT 2 21-SEP-01 5 REVDAT 1 18-AUG-88 0 JRNL AUTH A.AGGARWAL,S.A.ISLAM,R.KURODA,M.R.SANDERSON, JRNL AUTH 2 S.NEIDLE,H.M.BERMAN JRNL TITL THE STRUCTURE OF THE RIBODINUCLEOSIDE JRNL TITL 2 MONOPHOSPHATE GUANYLYL-3',5'-CYTIDINE AS ITS JRNL TITL 3 AMMONIUM OCTAHYDRATE SALT JRNL REF ACTA CRYSTALLOGR.,SECT.B V. 39 98 1983 JRNL REFN ASTM ACBCAR DK ISSN 0567-7408 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 0.85 ANGSTROM. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELX-76 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 0.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.111 REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 40 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 9 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : NULL REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : NULL REMARK 3 NUMBER OF RESTRAINTS : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : NULL REMARK 3 ANGLE DISTANCES (A) : NULL REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : NULL REMARK 3 ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : NULL REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL REMARK 3 SIMILAR ADP COMPONENTS (A**2) : NULL REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : NULL REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 NULL COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998 REMARK 105 REMARK 105 THE PROTEIN DATA BANK HAS ADOPTED THE SACCHARIDE CHEMISTS REMARK 105 NOMENCLATURE FOR ATOMS OF THE DEOXYRIBOSE/RIBOSE MOIETY REMARK 105 RATHER THAN THAT OF THE NUCLEOSIDE CHEMISTS. THE RING REMARK 105 OXYGEN ATOM IS LABELLED O4* INSTEAD OF O1*. REMARK 106 REMARK 106 ALL HYDROGEN BONDS BETWEEN BASE PAIRS NOT MENTIONED IN REMARK 106 REMARKS 102 AND 103 FOLLOW THE CONVENTIONAL WATSON-CRICK REMARK 106 HYDROGEN BONDING PATTERN. THEY HAVE NOT BEEN PRESENTED ON REMARK 106 *CONECT* RECORDS IN THIS ENTRY. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5400 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : DIFFRACTOMETER REMARK 200 DETECTOR MANUFACTURER : ENRAF-NONIUS CAD4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 3098 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.850 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): NULL REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NH4 SULFATE REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 1/2+X,1/2+Y,Z REMARK 290 4555 1/2-X,1/2+Y,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 10.49350 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 8.23500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 10.49350 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 8.23500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT REMARK 300 WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR REMARK 300 INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). REMARK 350 REMARK 350 GENERATING THE BIOMOLECULE REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 20.98700 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 5 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 10 LIES ON A SPECIAL POSITION. REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 7 O HOH A 8 2555 1.78 REMARK 500 O HOH A 9 O HOH A 12 1554 1.90 REMARK 500 N4 C A 2 O HOH A 7 4545 1.94 REMARK 500 O HOH A 7 O HOH A 7 2555 2.14 SEQRES 1 A 2 G C HET NH4 A 3 1 HETNAM NH4 AMMONIUM ION FORMUL 2 NH4 H4 N1 1+ FORMUL 3 HOH *9(H2 O1) CRYST1 20.987 16.470 9.566 90.00 94.36 90.00 C 1 2 1 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.047649 0.000000 0.003633 0.00000 SCALE2 0.000000 0.060716 0.000000 0.00000 SCALE3 0.000000 0.000000 0.104840 0.00000 ATOM 1 O5* G A 1 3.959 -3.327 5.885 1.00 6.71 O ATOM 2 C5* G A 1 3.592 -2.322 6.839 1.00 6.32 C ATOM 3 C4* G A 1 4.139 -0.972 6.543 1.00 3.32 C ATOM 4 O4* G A 1 5.537 -0.988 6.925 1.00 3.24 O ATOM 5 C3* G A 1 4.144 -0.511 5.103 1.00 3.47 C ATOM 6 O3* G A 1 2.913 0.099 4.741 1.00 3.32 O ATOM 7 C2* G A 1 5.343 0.445 5.074 1.00 4.74 C ATOM 8 O2* G A 1 5.004 1.713 5.656 1.00 3.87 O ATOM 9 C1* G A 1 6.342 -0.313 6.000 1.00 4.74 C ATOM 10 N9 G A 1 7.133 -1.301 5.265 1.00 2.68 N ATOM 11 C8 G A 1 7.126 -2.668 5.361 1.00 7.11 C ATOM 12 N7 G A 1 7.887 -3.278 4.454 1.00 4.90 N ATOM 13 C5 G A 1 8.561 -2.207 3.873 1.00 4.11 C ATOM 14 C6 G A 1 9.683 -2.223 2.928 1.00 4.47 C ATOM 15 O6 G A 1 10.140 -3.212 2.432 1.00 4.50 O ATOM 16 N1 G A 1 9.986 -0.955 2.528 1.00 3.32 N ATOM 17 C2 G A 1 9.486 0.231 3.024 1.00 3.87 C ATOM 18 N2 G A 1 9.916 1.416 2.613 1.00 5.21 N ATOM 19 N3 G A 1 8.511 0.247 3.977 1.00 3.87 N ATOM 20 C4 G A 1 8.087 -0.988 4.311 1.00 4.74 C ATOM 21 P C A 2 2.350 0.000 3.254 1.00 4.18 P ANISOU 21 P C A 2 2700 8000 5500 -400 2700 300 P ATOM 22 O1P C A 2 1.093 0.758 3.281 1.00 8.13 O ATOM 23 O2P C A 2 2.327 -1.416 2.785 1.00 7.43 O ATOM 24 O5* C A 2 3.451 0.725 2.356 1.00 3.79 O ATOM 25 C5* C A 2 3.549 2.158 2.451 1.00 4.03 C ATOM 26 C4* C A 2 4.669 2.652 1.517 1.00 3.47 C ATOM 27 O4* C A 2 5.919 2.026 1.917 1.00 4.42 O ATOM 28 C3* C A 2 4.508 2.240 0.057 1.00 3.24 C ATOM 29 O3* C A 2 3.527 3.047 -0.572 1.00 4.34 O ATOM 30 C2* C A 2 5.933 2.520 -0.467 1.00 5.13 C ATOM 31 O2* C A 2 6.209 3.903 -0.515 1.00 7.34 O ATOM 32 C1* C A 2 6.701 1.993 0.744 1.00 4.42 C ATOM 33 N1 C A 2 7.222 0.609 0.515 1.00 3.79 N ATOM 34 C2 C A 2 8.315 0.478 -0.334 1.00 3.24 C ATOM 35 O2 C A 2 8.795 1.515 -0.849 1.00 3.71 O ATOM 36 N3 C A 2 8.757 -0.758 -0.620 1.00 3.40 N ATOM 37 C4 C A 2 8.158 -1.845 -0.191 1.00 3.95 C ATOM 38 N4 C A 2 8.563 -3.030 -0.553 1.00 4.74 N ATOM 39 C5 C A 2 6.980 -1.729 0.668 1.00 3.55 C ATOM 40 C6 C A 2 6.578 -0.494 0.982 1.00 3.16 C TER 41 C A 2 HETATM 42 N NH4 A 3 6.032 4.908 -2.871 1.00 10.26 N HETATM 43 O HOH A 4 2.299 2.586 6.457 1.00 6.32 O HETATM 44 O HOH A 5 -0.364 2.668 4.769 1.00 11.05 O HETATM 45 O HOH A 6 7.409 2.899 4.941 1.00 7.90 O HETATM 46 O HOH A 7 0.923 3.969 -0.544 1.00 23.67 O HETATM 47 O HOH A 8 -0.325 2.438 1.240 1.00 22.11 O HETATM 48 O HOH A 9 2.065 1.466 -0.114 1.00 25.27 O HETATM 49 O HOH A 10 10.857 6.259 -4.769 1.00 39.48 O HETATM 50 O HOH A 11 11.889 4.463 -6.200 1.00 33.95 O HETATM 51 O HOH A 12 0.707 0.296 8.069 1.00 31.58 O MASTER 212 0 1 0 0 0 0 6 50 1 0 1 END