Header list of 1ql5.pdb file
Complete list - 15 202 Bytes
HEADER DNA 24-AUG-99 1QL5 TITLE DNA DECAMER DUPLEX CONTAINING T5-T6 PHOTOADDUCT COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*CP*GP*CP*AP*TP*+TP*AP*CP*GP*C)- 3'); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: CYCLOBUTANE RING FORMED BETWEEN C5-C6(T5) AND C5- COMPND 6 C6(T6) DOUBLE BONDS; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (5'-D(*GP*CP*GP*TP*TP*AP*TP*GP*CP*G)-3'); COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES KEYWDS DNA, DEOXYRIBONUCLEIC ACID, DNA PHOTOPRODUCT, (6-4) ADDUCT, KEYWDS 2 MUTAGENESIS EXPDTA SOLUTION NMR MDLTYP MINIMIZED AVERAGE AUTHOR J.-H.LEE,G.-S.HWANG,B.-S.CHOI REVDAT 5 15-JAN-20 1QL5 1 LINK REVDAT 4 22-FEB-12 1QL5 1 JRNL REMARK VERSN REVDAT 3 02-FEB-10 1QL5 1 VERSN REVDAT 2 24-FEB-09 1QL5 1 VERSN REVDAT 1 10-APR-00 1QL5 0 JRNL AUTH J.-H.LEE,Y.-J.CHOI,B.-S.CHOI JRNL TITL SOLUTION STRUCTURE OF A DNA DECAMER DUPLEX CONTAINING THE 3' JRNL TITL 2 T.T BASE PAIR OF THE CIS-SYN CYCLOBUTANE PYRIMIDINE DIMER: JRNL TITL 3 IMPLICATION FOR THE MUTAGENIC PROPERTY OF THE CIS-SYN DIMER. JRNL REF NUCLEIC ACIDS RES. V. 28 1794 2000 JRNL REFN ISSN 0305-1048 JRNL PMID 10734199 JRNL DOI 10.1093/NAR/28.8.1794 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: MISMATCHED BASE PAIRING OF 3'-T OF CIS REMARK 3 -SYN DIMER WITH A RESIDUE. REFINEMENT DETAILS CAN BE FOUND IN REMARK 3 THE JRNL CITATION ABOVE. REMARK 4 REMARK 4 1QL5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 24-AUG-99. REMARK 100 THE DEPOSITION ID IS D_1290002968. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 274.0 REMARK 210 PH : 6.6 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : DMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR REMARK 210 METHOD USED : SIMULATED ANNEALING AND FULL REMARK 210 RELAXATION MATRIX REFINEMENT REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 8 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : LEAST RESTRAINT VIOLATION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: MEAN STRUCTURE. THE STRUCTURE WAS DETERMINED USING SA REMARK 210 METHOD WITH DISTANCE RESTRAINTS AND FULL RELAXATION MATRIX REMARK 210 REFINEMENT WITH NOE INTENSITY RESTRAINTS OF 50, 80, 160 MS REMARK 210 MIXING TIMES REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2040 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 3620 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 5.0 KCAL/MOL 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 HO5' DC A 1 OP1 DG A 2 1.55 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 DA B 16 N9 DA B 16 C4 0.039 REMARK 500 DT B 17 N1 DT B 17 C2 0.054 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 DC A 1 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 DC A 1 N1 - C2 - O2 ANGL. DEV. = 3.7 DEGREES REMARK 500 DG A 2 C3' - O3' - P ANGL. DEV. = 16.9 DEGREES REMARK 500 DC A 3 N1 - C2 - O2 ANGL. DEV. = 4.0 DEGREES REMARK 500 DC A 3 C3' - O3' - P ANGL. DEV. = 8.8 DEGREES REMARK 500 DA A 4 C3' - O3' - P ANGL. DEV. = 11.8 DEGREES REMARK 500 PBT A 5 C3' - O3' - P ANGL. DEV. = 24.0 DEGREES REMARK 500 DC A 8 N1 - C2 - O2 ANGL. DEV. = 3.9 DEGREES REMARK 500 DC A 8 C3' - O3' - P ANGL. DEV. = 9.6 DEGREES REMARK 500 DG A 9 C3' - O3' - P ANGL. DEV. = 11.9 DEGREES REMARK 500 DG B 11 N3 - C2 - N2 ANGL. DEV. = 4.9 DEGREES REMARK 500 DC B 12 N1 - C2 - O2 ANGL. DEV. = 4.0 DEGREES REMARK 500 DC B 12 C3' - O3' - P ANGL. DEV. = 7.4 DEGREES REMARK 500 DG B 13 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 DG B 13 C2 - N3 - C4 ANGL. DEV. = 3.6 DEGREES REMARK 500 DG B 13 C3' - O3' - P ANGL. DEV. = 8.9 DEGREES REMARK 500 DT B 14 C3' - C2' - C1' ANGL. DEV. = -5.6 DEGREES REMARK 500 DT B 14 O4' - C1' - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 DT B 14 C3' - O3' - P ANGL. DEV. = 13.4 DEGREES REMARK 500 DT B 15 C3' - O3' - P ANGL. DEV. = 7.7 DEGREES REMARK 500 DA B 16 C3' - O3' - P ANGL. DEV. = 12.6 DEGREES REMARK 500 DG B 18 C2 - N3 - C4 ANGL. DEV. = 3.3 DEGREES REMARK 500 DG B 18 C3' - O3' - P ANGL. DEV. = 11.6 DEGREES REMARK 500 DG B 20 P - O5' - C5' ANGL. DEV. = 12.3 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4412 RELATED DB: BMRB DBREF 1QL5 A 1 10 PDB 1QL5 1QL5 1 10 DBREF 1QL5 B 11 20 PDB 1QL5 1QL5 11 20 SEQRES 1 A 10 DC DG DC DA PBT PBT DA DC DG DC SEQRES 1 B 10 DG DC DG DT DT DA DT DG DC DG HET PBT A 5 32 HET PBT A 6 32 HETNAM PBT [3-HYDROXY-5-(5-METHYL-2,4-DIOXOTETRAHYDRO-1(2H)- HETNAM 2 PBT PYRIMIDINYL)TETRAHYDRO-2-FURANYL]METHYL DIHYDROGEN HETNAM 3 PBT PHOSPHATE FORMUL 1 PBT 2(C10 H17 N2 O8 P) LINK O3' DA A 4 P PBT A 5 1555 1555 1.60 LINK O3' PBT A 5 P PBT A 6 1555 1555 1.61 LINK C5 PBT A 5 C5 PBT A 6 1555 1555 1.65 LINK C6 PBT A 5 C6 PBT A 6 1555 1555 1.66 LINK O3' PBT A 6 P DA A 7 1555 1555 1.62 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000
Complete list - 15 202 Bytes