Header list of 1kb1.pdb file
Complete list - 23 202 Bytes
HEADER DNA 05-NOV-01 1KB1
TITLE SOLUTION STRUCTURE OF AN 11-MER DNA DUPLEX CONTAINING 6-THIOGUANINE
TITLE 2 OPPOSITE CYTOSINE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: 5'-D(*CP*GP*TP*AP*CP*(S6G)P*CP*AP*TP*GP*C)-3';
COMPND 3 CHAIN: A;
COMPND 4 ENGINEERED: YES;
COMPND 5 MOL_ID: 2;
COMPND 6 MOLECULE: 5'-D(*GP*CP*AP*TP*GP*CP*GP*TP*AP*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 THIOGUANINE, 6-THIOGUANINE, TG, 6TG, S6G, THIOPURINE, DOUBLE HELIX,
KEYWDS 2 B-FORM DNA, DNA
EXPDTA SOLUTION NMR
AUTHOR J.BOHON,C.R.DE LOS SANTOS
REVDAT 4 23-FEB-22 1KB1 1 REMARK LINK
REVDAT 3 24-FEB-09 1KB1 1 VERSN
REVDAT 2 21-DEC-04 1KB1 1 AUTHOR JRNL REMARK MASTER
REVDAT 1 28-NOV-01 1KB1 0
JRNL AUTH J.BOHON,C.R.DE LOS SANTOS
JRNL TITL STRUCTURAL EFFECT OF THE ANTICANCER AGENT 6-THIOGUANINE ON
JRNL TITL 2 DUPLEX DNA.
JRNL REF NUCLEIC ACIDS RES. V. 31 1331 2003
JRNL REFN ISSN 0305-1048
JRNL PMID 12582253
JRNL DOI 10.1093/NAR/GKG203
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : FELIX 95 AND 98, X-PLOR 3.857
REMARK 3 AUTHORS : BIOSYM TECHNOLOGIES, INC. (FELIX), BRUNGER (X
REMARK 3 -PLOR)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 1KB1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-NOV-01.
REMARK 100 THE DEPOSITION ID IS D_1000014768.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 298; 276
REMARK 210 PH : 6.78; 6.78
REMARK 210 IONIC STRENGTH : 25 MM PHOSPHATE, 50 MM NACL, 0.5
REMARK 210 MM EDTA; 25 MM PHOSPHATE, 50 MM
REMARK 210 NACL, 0.5 MM EDTA
REMARK 210 PRESSURE : AMBIENT; AMBIENT
REMARK 210 SAMPLE CONTENTS : 2.4MM DNA 25MM PHOSPHATE BUFFER,
REMARK 210 50MM NACL, 0.5MM EDTA; 2.4MM DNA
REMARK 210 25MM PHOSPHATE BUFFER, 50MM NACL,
REMARK 210 0.5MM EDTA
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; COSY; DQF-COSY;
REMARK 210 COSY45; TOCSY; HETCO
REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 500 MHZ
REMARK 210 SPECTROMETER MODEL : INOVA
REMARK 210 SPECTROMETER MANUFACTURER : VARIAN
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : X-PLOR 3.857
REMARK 210 METHOD USED : RESTRAINED MOLECULAR DYNAMICS
REMARK 210 SIMULATIONS
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1
REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL
REMARK 210
REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING PROTON NMR FOLLOWED BY
REMARK 210 DISTANCE RESTRAINED MOLECULAR DYNAMICS SIMULATIONS, AND FURTHER
REMARK 210 REFINED BY THE FULL- RELAXATION MATRIX BACK CALCULATION METHOD.
REMARK 210 15 STRUCTURES EACH WERE DETERMINED FROM A- AND B-FORM DNA
REMARK 210 STARTING STRUCTURES. FIVE DIFFERENT STARTING TEMPERATURES AND
REMARK 210 THREE DIFFERENT LENGTHS OF TIME SPENT AT THE HIGH- TEMPERATURE
REMARK 210 STEP MAKE UP THE 15 STRUCTURES. 25 OF THE 30 TOTAL STRUCTURES
REMARK 210 CONVERGED TO AN RMSD OF .59A OR LESS. THE AVERAGE OF THESE 25
REMARK 210 STRUCTURES WAS CALCULATED AND UTILIZED IN THE FULL RELAXATION
REMARK 210 MATRIX BACK CALCULATIONS. THE MINIMIZED AVERAGE STRUCTURE FROM
REMARK 210 THIS LAST STEP IS THE FORM THAT IS DEPOSITED HERE.
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 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 DC A 1 C4 DC A 1 N4 0.095
REMARK 500 DG A 2 C2 DG A 2 N2 0.081
REMARK 500 DT A 3 C5 DT A 3 C7 0.037
REMARK 500 DA A 4 C6 DA A 4 N6 0.094
REMARK 500 DC A 5 C4 DC A 5 N4 0.094
REMARK 500 DC A 7 C4 DC A 7 N4 0.095
REMARK 500 DA A 8 C6 DA A 8 N6 0.094
REMARK 500 DT A 9 C5 DT A 9 C7 0.037
REMARK 500 DG A 10 C2 DG A 10 N2 0.079
REMARK 500 DC A 11 C4 DC A 11 N4 0.094
REMARK 500 DG B 1 C2 DG B 1 N2 0.079
REMARK 500 DC B 2 C4 DC B 2 N4 0.094
REMARK 500 DA B 3 C6 DA B 3 N6 0.093
REMARK 500 DT B 4 C5 DT B 4 C7 0.037
REMARK 500 DG B 5 C2 DG B 5 N2 0.080
REMARK 500 DC B 6 C4 DC B 6 N4 0.094
REMARK 500 DG B 7 C2 DG B 7 N2 0.083
REMARK 500 DT B 8 C5 DT B 8 C7 0.037
REMARK 500 DA B 9 C6 DA B 9 N6 0.093
REMARK 500 DC B 10 C4 DC B 10 N4 0.096
REMARK 500 DG B 11 C2 DG B 11 N2 0.086
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 DG A 2 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES
REMARK 500 DG A 2 N7 - C8 - N9 ANGL. DEV. = 3.1 DEGREES
REMARK 500 DA A 4 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES
REMARK 500 DC A 5 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES
REMARK 500 DG A 10 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES
REMARK 500 DG B 1 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES
REMARK 500 DG B 1 N7 - C8 - N9 ANGL. DEV. = 3.1 DEGREES
REMARK 500 DT B 4 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES
REMARK 500 DG B 5 N7 - C8 - N9 ANGL. DEV. = 3.0 DEGREES
REMARK 500 DG B 7 N7 - C8 - N9 ANGL. DEV. = 3.1 DEGREES
REMARK 500 DG B 11 N7 - C8 - N9 ANGL. DEV. = 3.0 DEGREES
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1KBM RELATED DB: PDB
REMARK 900 SOLUTION STRUCTURE OF AN 11-MER DNA DUPLEX CONTAINING 6-THIOGUANINE
REMARK 900 OPPOSITE THYMINE
DBREF 1KB1 A 1 11 PDB 1KB1 1KB1 1 11
DBREF 1KB1 B 1 11 PDB 1KB1 1KB1 1 11
SEQRES 1 A 11 DC DG DT DA DC S6G DC DA DT DG DC
SEQRES 1 B 11 DG DC DA DT DG DC DG DT DA DC DG
MODRES 1KB1 S6G A 6 DG
HET S6G A 6 33
HETNAM S6G 6-THIO-2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE
FORMUL 1 S6G C10 H14 N5 O6 P S
LINK O3' DC A 5 P S6G A 6 1555 1555 1.62
LINK O3' S6G A 6 P DC 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 - 23 202 Bytes