Header list of 1s37.pdb file
Complete list - 22 201 Bytes
HEADER DNA 12-JAN-04 1S37
TITLE ACCOMODATION OF MISPAIR-ALIGNED N3T-ETHYL-N3T DNA INTERSTRAND
TITLE 2 CROSSLINK
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: DNA (5'-D(*CP*GP*AP*AP*AP*(TTM)P*TP*TP*TP*CP*G)-3');
COMPND 3 CHAIN: A;
COMPND 4 ENGINEERED: YES;
COMPND 5 MOL_ID: 2;
COMPND 6 MOLECULE: DNA (5'-D(*CP*GP*AP*AP*AP*TP*TP*TP*TP*CP*G)-3');
COMPND 7 CHAIN: B;
COMPND 8 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 MOL_ID: 2;
SOURCE 4 SYNTHETIC: YES
KEYWDS INTERSTRAND CROSSLINK, DNA INTERSTRAND CROSS-LINK, DNA
EXPDTA SOLUTION NMR
MDLTYP MINIMIZED AVERAGE
AUTHOR M.W.DA SILVA,A.M.NORONHA,D.M.NOLL,P.S.MILLER,O.M.COLVIN,M.P.GAMCSIK
REVDAT 3 30-JUL-14 1S37 1 ATOM DBREF SEQRES VERSN
REVDAT 2 24-FEB-09 1S37 1 VERSN
REVDAT 1 25-JAN-05 1S37 0
JRNL AUTH M.W.DA SILVA,C.J.WILDS,A.M.NORONHA,O.M.COLVIN,P.S.MILLER,
JRNL AUTH 2 M.P.GAMCSIK
JRNL TITL ACCOMMODATION OF MISPAIR ALIGNED N3T-ETHYL-N3T DNA
JRNL TITL 2 INTERSTRAND CROSS LINK.
JRNL REF BIOCHEMISTRY V. 43 12549 2004
JRNL REFN ISSN 0006-2960
JRNL PMID 15449944
JRNL DOI 10.1021/BI0486435
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : X-PLOR 3.2
REMARK 3 AUTHORS : A.T. BRUNGER
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 1S37 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-JAN-04.
REMARK 100 THE RCSB ID CODE IS RCSB021309.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 273; 298
REMARK 210 PH : 7.4; 7.4
REMARK 210 IONIC STRENGTH : 0.1 MM NACL; 0.1 MM NACL
REMARK 210 PRESSURE : NORMAL; NORMAL
REMARK 210 SAMPLE CONTENTS : 100 MM NACL, PH 7.4 ADJUSTED
REMARK 210 WITH PHOSPHATE BUFFER
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 2D TOCSY; DQF-COSY
REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ
REMARK 210 SPECTROMETER MODEL : INOVA
REMARK 210 SPECTROMETER MANUFACTURER : VARIAN
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : FELIX 2000
REMARK 210 METHOD USED : DISTANCE GEOMETRY, SIMULATED
REMARK 210 ANNEALING, MOLECULAR DYNAMICS
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 8
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1
REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST ENERGY
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 8
REMARK 210
REMARK 210 REMARK: STRUCTURE DETERMINED USING STANDARD NMR EXPERIMENTS.
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 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC
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: 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' - C2' ANGL. DEV. = -5.4 DEGREES
REMARK 500 DC A 1 O4' - C1' - N1 ANGL. DEV. = 6.1 DEGREES
REMARK 500 DG A 2 C3' - C2' - C1' ANGL. DEV. = -7.7 DEGREES
REMARK 500 DG A 2 O4' - C1' - C2' ANGL. DEV. = -5.3 DEGREES
REMARK 500 DA A 3 O4' - C1' - C2' ANGL. DEV. = -7.9 DEGREES
REMARK 500 DA A 3 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES
REMARK 500 DA A 3 C6 - N1 - C2 ANGL. DEV. = 4.0 DEGREES
REMARK 500 DA A 3 N1 - C6 - N6 ANGL. DEV. = 4.2 DEGREES
REMARK 500 DA A 4 C3' - C2' - C1' ANGL. DEV. = -5.2 DEGREES
REMARK 500 DA A 4 O4' - C1' - N9 ANGL. DEV. = 5.0 DEGREES
REMARK 500 DA A 4 N1 - C6 - N6 ANGL. DEV. = 3.8 DEGREES
REMARK 500 DA A 5 C4' - C3' - C2' ANGL. DEV. = -6.0 DEGREES
REMARK 500 DA A 5 N1 - C6 - N6 ANGL. DEV. = 3.8 DEGREES
REMARK 500 DT A 7 C3' - C2' - C1' ANGL. DEV. = -5.3 DEGREES
REMARK 500 DT A 7 O4' - C1' - C2' ANGL. DEV. = -6.6 DEGREES
REMARK 500 DT A 7 C4 - C5 - C6 ANGL. DEV. = 3.8 DEGREES
REMARK 500 DT A 7 C4 - C5 - C7 ANGL. DEV. = 3.6 DEGREES
REMARK 500 DT A 7 C6 - C5 - C7 ANGL. DEV. = -7.3 DEGREES
REMARK 500 DT A 8 O4' - C1' - C2' ANGL. DEV. = -4.9 DEGREES
REMARK 500 DT A 8 C4 - C5 - C6 ANGL. DEV. = 4.0 DEGREES
REMARK 500 DT A 8 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES
REMARK 500 DT A 9 C1' - O4' - C4' ANGL. DEV. = -6.1 DEGREES
REMARK 500 DT A 9 O4' - C1' - C2' ANGL. DEV. = -10.3 DEGREES
REMARK 500 DT A 9 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES
REMARK 500 DT A 9 C4 - C5 - C6 ANGL. DEV. = 3.7 DEGREES
REMARK 500 DT A 9 C6 - C5 - C7 ANGL. DEV. = -6.9 DEGREES
REMARK 500 DC A 10 C3' - C2' - C1' ANGL. DEV. = -8.0 DEGREES
REMARK 500 DC A 10 O4' - C1' - C2' ANGL. DEV. = -5.1 DEGREES
REMARK 500 DC A 10 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES
REMARK 500 DC A 10 N1 - C2 - O2 ANGL. DEV. = 4.1 DEGREES
REMARK 500 DG A 11 O4' - C4' - C3' ANGL. DEV. = -5.2 DEGREES
REMARK 500 DG A 11 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES
REMARK 500 DC B 1 O4' - C1' - C2' ANGL. DEV. = -5.7 DEGREES
REMARK 500 DC B 1 O4' - C1' - N1 ANGL. DEV. = 5.8 DEGREES
REMARK 500 DG B 2 C3' - C2' - C1' ANGL. DEV. = -7.5 DEGREES
REMARK 500 DG B 2 O4' - C1' - C2' ANGL. DEV. = -5.5 DEGREES
REMARK 500 DA B 3 O4' - C1' - C2' ANGL. DEV. = -8.0 DEGREES
REMARK 500 DA B 3 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES
REMARK 500 DA B 3 C6 - N1 - C2 ANGL. DEV. = 3.9 DEGREES
REMARK 500 DA B 3 N1 - C6 - N6 ANGL. DEV. = 4.2 DEGREES
REMARK 500 DA B 4 C3' - C2' - C1' ANGL. DEV. = -5.4 DEGREES
REMARK 500 DA B 4 O4' - C1' - N9 ANGL. DEV. = 5.0 DEGREES
REMARK 500 DA B 4 N1 - C6 - N6 ANGL. DEV. = 3.8 DEGREES
REMARK 500 DA B 5 C4' - C3' - C2' ANGL. DEV. = -5.6 DEGREES
REMARK 500 DA B 5 N1 - C6 - N6 ANGL. DEV. = 3.8 DEGREES
REMARK 500 DT B 6 C6 - C5 - C7 ANGL. DEV. = -6.4 DEGREES
REMARK 500 DT B 7 C3' - C2' - C1' ANGL. DEV. = -5.3 DEGREES
REMARK 500 DT B 7 O4' - C1' - C2' ANGL. DEV. = -7.2 DEGREES
REMARK 500 DT B 7 C4 - C5 - C6 ANGL. DEV. = 3.7 DEGREES
REMARK 500 DT B 7 C6 - C5 - C7 ANGL. DEV. = -6.5 DEGREES
REMARK 500
REMARK 500 THIS ENTRY HAS 63 ANGLE DEVIATIONS.
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CHIRAL CENTERS
REMARK 500
REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL
REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY
REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR
REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE
REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16)
REMARK 500
REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS
REMARK 500 DT A 9 -45.7 D D OUTSIDE RANGE
REMARK 500 DT B 9 -45.8 D D OUTSIDE RANGE
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1N74 RELATED DB: PDB
REMARK 900 DNA INTERSTRAND CROSSLINK
REMARK 900 RELATED ID: 1N4B RELATED DB: PDB
REMARK 900 DNA INTERSTRAND CROSSLINK
DBREF 1S37 A 1 11 PDB 1S37 1S37 1 11
DBREF 1S37 B 1 11 PDB 1S37 1S37 1 11
SEQRES 1 A 11 DC DG DA DA DA TTM DT DT DT DC DG
SEQRES 1 B 11 DC DG DA DA DA DT DT DT DT DC DG
MODRES 1S37 TTM A 6 DT N3-ETHYL-THYMIDINE-5'-MONOPHOSPHATE
HET TTM A 6 37
HETNAM TTM N3-ETHYL-THYMIDINE-5'-MONOPHOSPHATE
FORMUL 1 TTM C12 H19 N2 O8 P
LINK O3' DA A 5 P TTM A 6 1555 1555 1.59
LINK O3' TTM A 6 P DT A 7 1555 1555 1.59
LINK C2Q TTM A 6 N3 DT B 6 1555 1555 1.48
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 - 22 201 Bytes