HEADER RIBONUCLEIC ACID 04-OCT-94 URB020 TITLE THE CRYSTAL AND MOLECULAR STRUCTURE OF A DINUCLEOSIDE TITLE 2 PHOSPHATE: BETA-ADENOSINE-2'-BETA-URIDINE-5'-PHOSPHORIC ACI COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (5'-R(*AP*U)-3'); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS U-RNA, SINGLE STRAND, OPEN EXPDTA X-RAY DIFFRACTION AUTHOR E.SHEFTER,M.BARLOW,R.A.SPARKS,K.N.TRUEBLOOD REVDAT 2 21-SEP-01 5 REVDAT 1 04-OCT-94 0 JRNL AUTH E.SHEFTER,M.BARLOW,R.A.SPARKS,K.N.TRUEBLOOD JRNL TITL THE CRYSTAL AND MOLECULAR STRUCTURE OF A JRNL TITL 2 DINUCLEOSIDE PHOSPHATE: BETA- JRNL TITL 3 ADENOSINE-2'-BETA-URIDINE-5'-PHOSPHORIC ACID JRNL REF ACTA CRYSTALLOGR.,SECT.B V. 25 895 1969 JRNL REFN ASTM ACBCAR DK ISSN 0567-7408 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. NULL ANGSTROM. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : NULL REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : NULL REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 1781 REMARK 3 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.060 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 39 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 3 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : NULL REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : 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 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 : OSCILLATION CAMERA REMARK 200 DETECTOR MANUFACTURER : WEISSENBERG REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL 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: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -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 8.00650 REMARK 290 SMTRY3 2 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI REMARK 500 O2* A A 1 P U A 2 1.59 REMARK 525 REMARK 525 SOLVENT REMARK 525 THE FOLLOWING SOLVENT MOLECULES LIE FARTHER THAN EXPECTED REMARK 525 FROM THE PROTEIN OR NUCLEIC ACID MOLECULE AND MAY BE REMARK 525 ASSOCIATED WITH A SYMMETRY RELATED MOLECULE (M=MODEL REMARK 525 NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 0 HOH 3 DISTANCE = 6.57 ANGSTROMS SEQRES 1 A 2 A U FORMUL 2 HOH *3(H2 O1) CRYST1 9.783 16.013 8.718 90.00 90.79 90.00 P 1 21 1 2 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 0.102218 0.000000 0.001409 0.00000 SCALE2 0.000000 0.062449 0.000000 0.00000 SCALE3 0.000000 0.000000 0.114716 0.00000 ATOM 1 O5* A A 1 0.637 3.456 5.458 1.00 10.00 O ATOM 2 C5* A A 1 0.370 2.743 6.677 1.00 10.00 C ATOM 3 C4* A A 1 -0.238 1.400 6.407 1.00 10.00 C ATOM 4 O4* A A 1 -1.612 1.614 5.974 1.00 10.00 O ATOM 5 C3* A A 1 0.448 0.568 5.270 1.00 10.00 C ATOM 6 O3* A A 1 0.323 -0.826 5.590 1.00 10.00 O ATOM 7 C2* A A 1 -0.493 0.868 4.124 1.00 10.00 C ATOM 8 O2* A A 1 -0.477 -0.167 3.136 1.00 10.00 O ATOM 9 C1* A A 1 -1.839 0.884 4.786 1.00 10.00 C ATOM 10 N9 A A 1 -2.923 1.512 4.065 1.00 10.00 N ATOM 11 C8 A A 1 -3.052 2.839 3.654 1.00 10.00 C ATOM 12 N7 A A 1 -4.179 3.047 3.013 1.00 10.00 N ATOM 13 C5 A A 1 -4.793 1.803 2.962 1.00 10.00 C ATOM 14 C6 A A 1 -6.005 1.396 2.389 1.00 10.00 C ATOM 15 N6 A A 1 -6.829 2.165 1.701 1.00 10.00 N ATOM 16 N1 A A 1 -6.284 0.070 2.588 1.00 10.00 N ATOM 17 C2 A A 1 -5.469 -0.773 3.255 1.00 10.00 C ATOM 18 N3 A A 1 -4.332 -0.444 3.806 1.00 10.00 N ATOM 19 C4 A A 1 -4.023 0.857 3.611 1.00 10.00 C ATOM 20 P U A 2 0.012 0.035 1.633 1.00 10.00 P ATOM 21 O1P U A 2 1.207 -0.889 1.486 1.00 10.00 O ATOM 22 O2P U A 2 0.198 1.459 1.281 1.00 10.00 O ATOM 23 O5* U A 2 -1.207 -0.527 0.788 1.00 10.00 O ATOM 24 C5* U A 2 -1.846 -1.809 1.115 1.00 10.00 C ATOM 25 C4* U A 2 -3.102 -1.925 0.297 1.00 10.00 C ATOM 26 O4* U A 2 -4.004 -0.847 0.658 1.00 10.00 O ATOM 27 C3* U A 2 -2.998 -1.825 -1.216 1.00 10.00 C ATOM 28 O3* U A 2 -2.660 -3.026 -1.861 1.00 10.00 O ATOM 29 C2* U A 2 -4.413 -1.392 -1.614 1.00 10.00 C ATOM 30 O2* U A 2 -5.330 -2.474 -1.489 1.00 10.00 O ATOM 31 C1* U A 2 -4.729 -0.431 -0.472 1.00 10.00 C ATOM 32 N1 U A 2 -4.361 0.980 -0.811 1.00 10.00 N ATOM 33 C2 U A 2 -5.133 1.619 -1.726 1.00 10.00 C ATOM 34 O2 U A 2 -6.065 1.068 -2.321 1.00 10.00 O ATOM 35 N3 U A 2 -4.764 2.921 -2.005 1.00 10.00 N ATOM 36 C4 U A 2 -3.726 3.640 -1.378 1.00 10.00 C ATOM 37 O4 U A 2 -3.480 4.773 -1.761 1.00 10.00 O ATOM 38 C5 U A 2 -3.047 2.908 -0.342 1.00 10.00 C ATOM 39 C6 U A 2 -3.352 1.637 -0.110 1.00 10.00 C TER 40 U A 2 HETATM 41 O HOH 3 3.297 4.287 -3.781 1.00 10.00 O HETATM 42 O HOH 4 -1.759 6.008 1.017 1.00 10.00 O HETATM 43 O HOH 5 -1.215 5.223 -3.748 1.00 10.00 O MASTER 209 0 0 0 0 0 0 6 42 1 0 1 END