10 20 30 40 50 60 70 80 DRBB13 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER RIBONUCLEIC ACID 18-AUG-88 DRBB13
TITLE REPORTER MOLECULES AS PROBES OF DNA CONFORMATION: STRUCTURE TITLE 2 OF A CRYSTALLINE COMPLEX CONTAINING 2-METHYL-4- TITLE 3 NITROANILINE ETHYLENE DIMETHYLAMMONIUM HYDROBROMIDE-5- TITLE 4 IODOCYTIDYLYL(3'-5')GUANOSINE
COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (5'-R(*(I)CP*G)-3'); COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES
KEYWDS RIGHT HANDED RNA, DOUBLE HELIX, COMPLEXED WITH DRUG, KEYWDS 2 MODIFIED
EXPDTA X-RAY DIFFRACTION
AUTHOR N.K.VYAS,M.N.VYAS,S.C.JAIN,H.M.SOBELL
REVDAT 2 21-SEP-01 5 REVDAT 1 18-AUG-88 0
JRNL AUTH N.K.VYAS,M.N.VYAS,S.C.JAIN,H.M.SOBELL JRNL TITL REPORTER MOLECULES AS PROBES OF DNA CONFORMATION: JRNL TITL 2 STRUCTURE OF A CRYSTALLINE COMPLEX CONTAINING JRNL TITL 3 2-METHYL-4-NITROANILINE ETHYLENE DIMETHYLAMMONIUM JRNL TITL 4 HYDROBROMIDE-5-IODOCYTIDYLYL(3'-5')GUANOSINE JRNL REF BIOCHEM.BIOPHYS.RES.COMM. V. 121 188 1984 JRNL REFN ASTM BBRCA9 US ISSN 0006-291X
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 1.14 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.14 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 : 2002 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) : 0.114 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 : 80 REMARK 3 HETEROGEN ATOMS : 51 REMARK 3 SOLVENT ATOMS : 29 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 101 REMARK 101 RESIDUE +C A 1 HAS IDO BONDED TO C5. REMARK 101 RESIDUE +C B 3 HAS IDO BONDED TO C5.
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) : 275.0 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 : 4942 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.140 REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,1/2+Z REMARK 290 3555 1/2-Y,1/2+X,3/4+Z REMARK 290 4555 1/2+Y,1/2-X,1/4+Z REMARK 290 5555 1/2-X,1/2+Y,3/4-Z REMARK 290 6555 1/2+X,1/2-Y,1/4-Z REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,1/2-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 11.98200 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 16.09600 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 16.09600 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 17.97300 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 16.09600 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 16.09600 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 5.99100 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 16.09600 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 16.09600 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 17.97300 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 16.09600 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 16.09600 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 5.99100 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 11.98200 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 2 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 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 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 23 LIES ON A SPECIAL POSITION.
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 O HOH 29 O HOH 30 1.21 REMARK 500 O HOH 26 O HOH 27 1.28 REMARK 500 O HOH 24 O HOH 25 1.40
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 8 DISTANCE = 8.69 ANGSTROMS REMARK 525 0 HOH 12 DISTANCE = 5.04 ANGSTROMS REMARK 525 0 HOH 14 DISTANCE = 10.94 ANGSTROMS REMARK 525 0 HOH 22 DISTANCE = 9.97 ANGSTROMS REMARK 525 0 HOH 24 DISTANCE = 9.35 ANGSTROMS REMARK 525 0 HOH 25 DISTANCE = 9.51 ANGSTROMS REMARK 525 0 HOH 28 DISTANCE = 5.44 ANGSTROMS REMARK 525 0 HOH 32 DISTANCE = 9.01 ANGSTROMS REMARK 525 0 HOH 33 DISTANCE = 5.57 ANGSTROMS REMARK 525 0 HOH 34 DISTANCE = 10.36 ANGSTROMS
SEQRES 1 A 2 +C G SEQRES 1 B 2 +C G
MODRES +C A 1 C CYTOSINE MODIFIED WITH I MODRES +C B 3 C CYTOSINE MODIFIED WITH I
FTNOTE 1 THESE ATOMS ARE DISORDERED (A). FTNOTE 2 THESE ATOMS ARE DISORDERED (B). FTNOTE 3 THESE ATOMS ARE DISORDERED (C).
HET MNE 5 16 HET MNE 6 16 HET MNE 7 17 HET IDO A 1 1 HET IDO B 3 1
HETNAM MNE DIMETHYL-[2-[2-METHYL-4-NITRO-PHENYL-AMINO]-ETHYL]- HETNAM 2 MNE AMMONIUM HETNAM IDO IODO GROUP
FORMUL 3 MNE 3(C11 H18 N3 O2 1+) FORMUL 6 IDO 2(I1) FORMUL 8 HOH *29(H2 O1)
LINK I IDO A 1 C5 +C A 1 LINK I IDO B 3 C5 +C B 3
CRYST1 32.192 32.192 23.964 90.00 90.00 90.00 P 43 21 2 16
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 0.031066 0.000000 0.000000 0.00000
SCALE2 0.000000 0.031066 0.000000 0.00000
SCALE3 0.000000 0.000000 0.041736 0.00000