HEADER RIBONUCLEIC ACID 09-OCT-97 356D OBSLTE 28-JAN-98 356D 364D TITLE 3.0 A STRUCTURE OF FRAGMENT I FROM E. COLI 5S RRNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (5'-R(*UP*GP*)-D(*CP(S)*)- COMPND 3 R(*CP*UP*GP*GP*CP*GP*GP*C)-3'); COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: RNA (5'- COMPND 8 R(*CP*CP*GP*AP*UP*GP*GP*UP*AP*GP*UP*GP*UP*GP*GP*GP*G COMPND 9 *UP*C)-3'); COMPND 10 CHAIN: B; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: RNA (5'- COMPND 14 R(*CP*CP*CP*CP*AP*UP*GP*CP*GP*AP*GP*AP*GP*UP*AP*GP*G COMPND 15 P*GP*AP*AP*CP*UP*GP*CP*CP*AP*GP*GP*CP*AP*U)-3'); COMPND 16 CHAIN: C; COMPND 17 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES; SOURCE 5 MOL_ID: 3; SOURCE 6 SYNTHETIC: YES KEYWDS U-RNA, DOUBLE HELIX, KINKED, INTERNAL LOOP, OVERHANGING KEYWDS 2 BASE, MODIFIED, MISMATCHED, RIBONUCLEIC ACID EXPDTA X-RAY DIFFRACTION AUTHOR C.C.CORRELL,B.FREEBORN,P.B.MOORE,T.A.STEITZ REVDAT 1 31-DEC-97 356D 0 JRNL AUTH C.C.CORRELL,B.FREEBORN,P.B.MOORE,T.A.STEITZ JRNL TITL METALS, MOTIFS, AND RECOGNITION IN THE CRYSTAL JRNL TITL 2 STRUCTURE OF A 5S RRNA DOMAIN JRNL REF CELL(CAMBRIDGE,MASS.) V. 91 705 1997 JRNL REFN ASTM CELLB5 US ISSN 0092-8674 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH A.DALLAS,P.B.MOORE REMARK 1 TITL THE SOLUTION STRUCTURE OF THE LOOP E/LOOP D REGION REMARK 1 TITL 2 OF E. COLI 5S RRNA REMARK 1 REF TO BE PUBLISHED REMARK 1 REFN REMARK 1 REFERENCE 2 REMARK 1 AUTH C.C.CORRELL,B.FREEBORN,P.B.MOORE,T.A.STEITZ REMARK 1 TITL USE OF CHEMICALLY MODIFIED NUCLEOTIDES TO REMARK 1 TITL 2 DETERMINE A 62-NUCLEOTIDE RNA CRYSTAL STRUCTURE: A REMARK 1 TITL 3 SURVEY OF PHOSPHOROTHIOATES, BR, PT, AND HG REMARK 1 REF J.BIOMOL.STRUCT.DYN. V. 15 165 1997 REMARK 1 REFN ASTM JBSDD6 US ISSN 0739-1102 REMARK 2 REMARK 2 RESOLUTION. 3.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 525997.650 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 80.1 REMARK 3 NUMBER OF REFLECTIONS : 4668 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.268 REMARK 3 FREE R VALUE : 0.321 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.900 REMARK 3 FREE R VALUE TEST SET COUNT : 510 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.015 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 3.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.19 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 47.60 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 392 REMARK 3 BIN R VALUE (WORKING SET) : 0.4620 REMARK 3 BIN FREE R VALUE : 0.5120 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.10 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 47 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.070 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 1296 REMARK 3 HETEROGEN ATOMS : 14 REMARK 3 SOLVENT ATOMS : 4 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 87.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 83.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 10.96000 REMARK 3 B22 (A**2) : 10.96000 REMARK 3 B33 (A**2) : -21.90000 REMARK 3 B12 (A**2) : 16.98000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.54 REMARK 3 ESD FROM SIGMAA (A) : 0.52 REMARK 3 LOW RESOLUTION CUTOFF (A) : 20.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.74 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.80 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.10 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 29.70 REMARK 3 IMPROPER ANGLES (DEGREES) : 2.24 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) : 1.930 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 3.180 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.920 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.210 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL 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 : DNA-RNA-MULTI-ENDO.PARAM REMARK 3 PARAMETER FILE 2 : MG.PARAM REMARK 3 PARAMETER FILE 3 : PATCH.PAR REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : DNA-RNA-MULTI-ENDO.TOP REMARK 3 TOPOLOGY FILE 2 : MG.PARAM REMARK 3 TOPOLOGY FILE 3 : PATCH.PAR REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: TARGET FOR REFINEMENT WAS MLF: REMARK 3 MAXIMUM LIKELIHOOD TARGET USING AMPLITUDES REMARK 4 REMARK 4 356D COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998 REMARK 6 REMARK 6 THERE IS A DIASTEREOMERIC MIXTURE OF RP AND SP REMARK 6 PHOSPHOROTHIOATE AT RESIDUE C 4, THEREFORE BOTH O AND S REMARK 6 ARE AT 0.5 OCCUPANCY. REMARK 7 REMARK 7 NUCLEOTIDES 87 AND 88 ARE DISORDERED. REMARK 8 REMARK 8 NUCLEOTIDE 120 IS ONLY ORDERED FOR THE PHOSPHATE GROUP. REMARK 8 THE OTHER ATOMS ARE MISSING. REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY THE NUCLEIC ACID DATABASE REMARK 100 ON 10-OCT-1997. REMARK 100 THE NDB ID CODE IS URL065. 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 : 28-MAR-1995 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 6.40 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CHESS REMARK 200 BEAMLINE : A1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.92 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : SILICON 111 BENDING MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : PRINCETON 2K REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4950 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.980 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 82.5 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : 0.04700 REMARK 200 R SYM (I) : 0.04700 REMARK 200 FOR THE DATA SET : 10.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.98 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.09 REMARK 200 COMPLETENESS FOR SHELL (%) : 47.5 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : 0.37200 REMARK 200 R SYM FOR SHELL (I) : 0.37000 REMARK 200 FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 6.4 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,1/3+Z REMARK 290 3555 -X+Y,-X,2/3+Z REMARK 290 4555 -X,-Y,1/2+Z REMARK 290 5555 Y,-X+Y,5/6+Z REMARK 290 6555 X-Y,X,1/6+Z REMARK 290 7555 Y,X,1/3-Z REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,2/3-Z REMARK 290 10555 -Y,-X,5/6-Z REMARK 290 11555 -X+Y,Y,1/2-Z REMARK 290 12555 X,X-Y,1/6-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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 84.69000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 169.38000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 127.03500 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 211.72500 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 42.34500 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 84.69000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 169.38000 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 211.72500 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 127.03500 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 42.34500 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 3 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, B, C 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS(M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 +C A 4 O2P REMARK 470 U C 120 C5* C4* O4* C3* O3* C2* C1* REMARK 470 U C 120 N1 C2 O2 N3 C4 O4 C5 REMARK 470 U C 120 C6 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 O1P +C A 4 S S A 4 0.39 REMARK 500 O1P +C A 4 S S A 4 0.39 DBREF 356D A 1 11 NDB URL065 URL065 1 11 DBREF 356D B 32 50 NDB URL065 URL065 12 30 DBREF 356D C 51 81 NDB URL065 URL065 31 61 SEQRES 1 A 11 U G C +C U G G C G G C SEQRES 1 B 19 C C G A U G G U A G U G U SEQRES 2 B 19 G G G G U C SEQRES 1 C 31 C C C C A U G C G A G A G SEQRES 2 C 31 U A G G G A A C U G C C A SEQRES 3 C 31 G G C A U MODRES 356D +C A 4 C CYTOSINE MODIFIED WITH S HET MG 201 1 HET MG 202 1 HET MG 204 1 HET MG 205 1 HET MG 207 1 HET MG 208 1 HET MG 209 1 HET MG 210 1 HET MG 211 1 HET MG 213 1 HET MG 214 1 HET MG 216 1 HET S A 4 2 HETNAM MG MAGNESIUM ION HETNAM S SULFUR ATOM FORMUL 4 MG 12(MG 2+) FORMUL 16 S S FORMUL 17 HOH *4(H2 O1) LINK S A S A 4 P +C A 4 LINK S B S A 4 P +C A 4 CRYST1 59.030 59.030 254.070 90.00 90.00 120.00 P 61 2 2 12 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 0.016941 0.009781 0.000000 0.00000 SCALE2 0.000000 0.019561 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003936 0.00000