Header list of 1sy8.pdb file
Complete list - 25 20 Bytes
HEADER DNA 01-APR-04 1SY8
TITLE STRUCTURE OF DNA SEQUENCE D-TGATCA BY TWO-DIMENSIONAL NUCLEAR MAGNETIC
TITLE 2 RESONANCE SPEC AND RESTRAINED MOLECULAR DYNAMICS
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: 5'-D(P*TP*GP*AP*TP*CP*A)-3';
COMPND 3 CHAIN: A, B;
COMPND 4 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES
KEYWDS TPG/CPA BASEPAIR STEP, 2D-NMR OF D-TGATCA, RESTRAINED MOLECULAR
KEYWDS 2 DYNAMICS, SEQUENCE RELATED CONFORMATION, DNA FLEXIBILITY, DNA
EXPDTA SOLUTION NMR
NUMMDL 10
AUTHOR R.BARTHWAL,P.AWASTHI,M.NARANG,U.SHARMA,N.SRIVASTAVA
REVDAT 3 22-FEB-12 1SY8 1 JRNL VERSN
REVDAT 2 24-FEB-09 1SY8 1 VERSN
REVDAT 1 04-JAN-05 1SY8 0
JRNL AUTH R.BARTHWAL,P.AWASTHI,M.NARANG,M.KAUR,U.SHARMA,N.SRIVASTAVA,
JRNL AUTH 2 S.K.BARTHWAL,G.GOVIL
JRNL TITL STRUCTURE OF DNA SEQUENCE D-TGATCA BY TWO-DIMENSIONAL
JRNL TITL 2 NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY AND RESTRAINED
JRNL TITL 3 MOLECULAR DYNAMICS
JRNL REF J.STRUCT.BIOL. V. 148 34 2004
JRNL REFN ISSN 1047-8477
JRNL PMID 15363786
JRNL DOI 10.1016/J.JSB.2004.05.005
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : DISCOVER 97
REMARK 3 AUTHORS : MOLECULAR SIMULATIONS INC.
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURE IS BASED ON TOTAL 95
REMARK 3 INTRA RESIDUE AND 26 INTER RESIDUE NOESY RESTRAINTS AND 12
REMARK 3 TORSINAL ANGLE RESTRAINTS.
REMARK 4
REMARK 4 1SY8 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 09-APR-04.
REMARK 100 THE RCSB ID CODE IS RCSB022089.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 295
REMARK 210 PH : 7.0
REMARK 210 IONIC STRENGTH : 20MM PHOSPHATE BUFFER; 15MM NACL
REMARK 210 PRESSURE : AMBIENT
REMARK 210 SAMPLE CONTENTS : 3.68MM DUPLEX CONCENTRATION;
REMARK 210 20MM PHOSPHATE BUFFER WITH 15MM
REMARK 210 NACL; 4.57MM DUPLEX
REMARK 210 CONCENTRATION; 20MM PHOSPHATE
REMARK 210 BUFFER WITH 15MM NACL
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; DQF-COSY
REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ
REMARK 210 SPECTROMETER MODEL : AM
REMARK 210 SPECTROMETER MANUFACTURER : BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : NULL
REMARK 210 METHOD USED : SIMULATED ANNEALING, MOLECULAR
REMARK 210 DYNAMICS
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 25
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10
REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH ACCEPTABLE
REMARK 210 COVALENT GEOMETRY
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1
REMARK 210
REMARK 210 REMARK: FOR IMINO PROTONS 1D WATER SPECTRA VS TEMPERATURE WAS ALSO
REMARK 210 DONE
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 1 DT A 1 C5' DT A 1 C4' 0.044
REMARK 500 1 DC A 5 C4 DC A 5 N4 0.070
REMARK 500 1 DT B 1 C5' DT B 1 C4' 0.042
REMARK 500 1 DC B 5 C4 DC B 5 N4 0.070
REMARK 500 2 DT A 1 C5' DT A 1 C4' 0.043
REMARK 500 2 DC A 5 C4 DC A 5 N4 0.070
REMARK 500 2 DT B 1 C5' DT B 1 C4' 0.044
REMARK 500 2 DC B 5 C4 DC B 5 N4 0.070
REMARK 500 3 DT A 1 C5' DT A 1 C4' 0.043
REMARK 500 3 DC A 5 C4 DC A 5 N4 0.070
REMARK 500 3 DC B 5 C4 DC B 5 N4 0.070
REMARK 500 4 DT A 1 C5' DT A 1 C4' 0.044
REMARK 500 4 DC A 5 C4 DC A 5 N4 0.070
REMARK 500 4 DC B 5 C4 DC B 5 N4 0.070
REMARK 500 5 DC A 5 C4 DC A 5 N4 0.069
REMARK 500 5 DC B 5 C4 DC B 5 N4 0.069
REMARK 500 5 DA B 6 N7 DA B 6 C8 0.056
REMARK 500 6 DC A 5 C4 DC A 5 N4 0.069
REMARK 500 6 DC B 5 C4 DC B 5 N4 0.069
REMARK 500 6 DA B 6 N7 DA B 6 C8 0.060
REMARK 500 7 DC A 5 C4 DC A 5 N4 0.070
REMARK 500 7 DC B 5 C4 DC B 5 N4 0.070
REMARK 500 8 DC A 5 C4 DC A 5 N4 0.069
REMARK 500 8 DC B 5 C4 DC B 5 N4 0.069
REMARK 500 9 DT A 1 C5' DT A 1 C4' 0.043
REMARK 500 9 DC A 5 C4 DC A 5 N4 0.069
REMARK 500 9 DC B 5 C4 DC B 5 N4 0.069
REMARK 500 10 DT A 1 C5' DT A 1 C4' 0.042
REMARK 500 10 DC A 5 C4 DC A 5 N4 0.070
REMARK 500 10 DC B 5 C4 DC B 5 N4 0.069
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 1 DT A 1 O5' - P - OP1 ANGL. DEV. = 8.4 DEGREES
REMARK 500 1 DT A 1 O5' - P - OP2 ANGL. DEV. = 8.3 DEGREES
REMARK 500 1 DT A 1 C4 - C5 - C7 ANGL. DEV. = 6.1 DEGREES
REMARK 500 1 DT A 1 C6 - C5 - C7 ANGL. DEV. = -8.8 DEGREES
REMARK 500 1 DG A 2 OP1 - P - OP2 ANGL. DEV. = -9.3 DEGREES
REMARK 500 1 DG A 2 N1 - C6 - O6 ANGL. DEV. = 4.0 DEGREES
REMARK 500 1 DG A 2 C5 - C6 - O6 ANGL. DEV. = -4.0 DEGREES
REMARK 500 1 DA A 3 OP1 - P - OP2 ANGL. DEV. = -9.1 DEGREES
REMARK 500 1 DA A 3 O4' - C4' - C3' ANGL. DEV. = 7.0 DEGREES
REMARK 500 1 DA A 3 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES
REMARK 500 1 DT A 4 OP1 - P - OP2 ANGL. DEV. = -9.1 DEGREES
REMARK 500 1 DT A 4 O4' - C4' - C3' ANGL. DEV. = 5.6 DEGREES
REMARK 500 1 DT A 4 O4' - C1' - N1 ANGL. DEV. = 5.9 DEGREES
REMARK 500 1 DT A 4 C6 - C5 - C7 ANGL. DEV. = -5.2 DEGREES
REMARK 500 1 DC A 5 OP1 - P - OP2 ANGL. DEV. = -9.2 DEGREES
REMARK 500 1 DC A 5 O4' - C4' - C3' ANGL. DEV. = 5.7 DEGREES
REMARK 500 1 DC A 5 C4' - C3' - C2' ANGL. DEV. = -4.3 DEGREES
REMARK 500 1 DC A 5 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES
REMARK 500 1 DA A 6 OP1 - P - OP2 ANGL. DEV. = -9.3 DEGREES
REMARK 500 1 DT B 1 O5' - P - OP1 ANGL. DEV. = 8.5 DEGREES
REMARK 500 1 DT B 1 O5' - P - OP2 ANGL. DEV. = 8.7 DEGREES
REMARK 500 1 DT B 1 C4 - C5 - C7 ANGL. DEV. = 7.0 DEGREES
REMARK 500 1 DT B 1 C6 - C5 - C7 ANGL. DEV. = -9.8 DEGREES
REMARK 500 1 DG B 2 OP1 - P - OP2 ANGL. DEV. = -9.3 DEGREES
REMARK 500 1 DG B 2 N1 - C6 - O6 ANGL. DEV. = 4.0 DEGREES
REMARK 500 1 DG B 2 C5 - C6 - O6 ANGL. DEV. = -4.0 DEGREES
REMARK 500 1 DA B 3 OP1 - P - OP2 ANGL. DEV. = -9.1 DEGREES
REMARK 500 1 DA B 3 O4' - C4' - C3' ANGL. DEV. = 6.5 DEGREES
REMARK 500 1 DA B 3 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES
REMARK 500 1 DT B 4 OP1 - P - OP2 ANGL. DEV. = -9.0 DEGREES
REMARK 500 1 DT B 4 O4' - C4' - C3' ANGL. DEV. = 5.3 DEGREES
REMARK 500 1 DT B 4 O4' - C1' - N1 ANGL. DEV. = 5.9 DEGREES
REMARK 500 1 DT B 4 C6 - C5 - C7 ANGL. DEV. = -6.0 DEGREES
REMARK 500 1 DC B 5 OP1 - P - OP2 ANGL. DEV. = -9.1 DEGREES
REMARK 500 1 DC B 5 O4' - C4' - C3' ANGL. DEV. = 5.6 DEGREES
REMARK 500 1 DC B 5 C4' - C3' - C2' ANGL. DEV. = -4.2 DEGREES
REMARK 500 1 DC B 5 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES
REMARK 500 1 DA B 6 OP1 - P - OP2 ANGL. DEV. = -9.3 DEGREES
REMARK 500 2 DT A 1 O5' - P - OP1 ANGL. DEV. = 8.0 DEGREES
REMARK 500 2 DT A 1 O5' - P - OP2 ANGL. DEV. = 8.1 DEGREES
REMARK 500 2 DT A 1 C4 - C5 - C7 ANGL. DEV. = 6.3 DEGREES
REMARK 500 2 DT A 1 C6 - C5 - C7 ANGL. DEV. = -9.0 DEGREES
REMARK 500 2 DG A 2 OP1 - P - OP2 ANGL. DEV. = -9.2 DEGREES
REMARK 500 2 DG A 2 N1 - C6 - O6 ANGL. DEV. = 4.0 DEGREES
REMARK 500 2 DG A 2 C5 - C6 - O6 ANGL. DEV. = -4.0 DEGREES
REMARK 500 2 DA A 3 OP1 - P - OP2 ANGL. DEV. = -9.1 DEGREES
REMARK 500 2 DA A 3 O4' - C4' - C3' ANGL. DEV. = 6.7 DEGREES
REMARK 500 2 DA A 3 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES
REMARK 500 2 DT A 4 OP1 - P - OP2 ANGL. DEV. = -9.1 DEGREES
REMARK 500 2 DT A 4 O4' - C4' - C3' ANGL. DEV. = 5.3 DEGREES
REMARK 500
REMARK 500 THIS ENTRY HAS 361 ANGLE DEVIATIONS.
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: PLANAR GROUPS
REMARK 500
REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL
REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE
REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN
REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS
REMARK 500 AN RMSD GREATER THAN THIS VALUE
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 M RES CSSEQI RMS TYPE
REMARK 500 1 DT A 4 0.09 SIDE CHAIN
REMARK 500 1 DA A 6 0.07 SIDE CHAIN
REMARK 500 1 DA B 3 0.05 SIDE CHAIN
REMARK 500 1 DT B 4 0.09 SIDE CHAIN
REMARK 500 1 DA B 6 0.05 SIDE CHAIN
REMARK 500 2 DT A 4 0.10 SIDE CHAIN
REMARK 500 2 DA A 6 0.05 SIDE CHAIN
REMARK 500 2 DT B 1 0.07 SIDE CHAIN
REMARK 500 2 DT B 4 0.09 SIDE CHAIN
REMARK 500 2 DA B 6 0.05 SIDE CHAIN
REMARK 500 3 DT A 1 0.08 SIDE CHAIN
REMARK 500 3 DA A 3 0.05 SIDE CHAIN
REMARK 500 3 DT A 4 0.10 SIDE CHAIN
REMARK 500 3 DA A 6 0.07 SIDE CHAIN
REMARK 500 3 DT B 4 0.10 SIDE CHAIN
REMARK 500 3 DA B 6 0.06 SIDE CHAIN
REMARK 500 4 DT A 1 0.07 SIDE CHAIN
REMARK 500 4 DA A 3 0.05 SIDE CHAIN
REMARK 500 4 DT A 4 0.10 SIDE CHAIN
REMARK 500 4 DT B 4 0.10 SIDE CHAIN
REMARK 500 5 DT A 4 0.10 SIDE CHAIN
REMARK 500 5 DT B 4 0.09 SIDE CHAIN
REMARK 500 6 DT A 4 0.09 SIDE CHAIN
REMARK 500 6 DA A 6 0.05 SIDE CHAIN
REMARK 500 6 DT B 1 0.06 SIDE CHAIN
REMARK 500 6 DT B 4 0.08 SIDE CHAIN
REMARK 500 7 DT A 1 0.06 SIDE CHAIN
REMARK 500 7 DT A 4 0.10 SIDE CHAIN
REMARK 500 7 DT B 1 0.06 SIDE CHAIN
REMARK 500 7 DT B 4 0.09 SIDE CHAIN
REMARK 500 7 DA B 6 0.06 SIDE CHAIN
REMARK 500 8 DT A 4 0.10 SIDE CHAIN
REMARK 500 8 DT B 1 0.07 SIDE CHAIN
REMARK 500 8 DT B 4 0.10 SIDE CHAIN
REMARK 500 9 DT A 4 0.09 SIDE CHAIN
REMARK 500 9 DT B 4 0.10 SIDE CHAIN
REMARK 500 9 DA B 6 0.06 SIDE CHAIN
REMARK 500 10 DT A 1 0.06 SIDE CHAIN
REMARK 500 10 DT A 4 0.08 SIDE CHAIN
REMARK 500 10 DA A 6 0.06 SIDE CHAIN
REMARK 500 10 DT B 4 0.10 SIDE CHAIN
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1D54 RELATED DB: PDB
REMARK 900 ANTHRACYCLINE BINDING TO DNA. HIGH-RESOLUTION STRUCTURE OF
REMARK 900 D(TGTACA) COMPLEXED WITH 4'-EPIADRIAMYCIN
REMARK 900 RELATED ID: 1D58 RELATED DB: PDB
REMARK 900 THE MOLECULAR STRUCTURE OF A 4'-EPIADRIAMYCIN COMPLEX WITH
REMARK 900 D(TGATCA) AT 1.7A RESOLUTION: COMPARISON WITH THE STRUCTURE
REMARK 900 OF 4'-EPIADRIAMYCIN D(TGTACA) AND D(CGATCG) COMPLEXES
DBREF 1SY8 A 1 6 PDB 1SY8 1SY8 1 6
DBREF 1SY8 B 1 6 PDB 1SY8 1SY8 1 6
SEQRES 1 A 6 DT DG DA DT DC DA
SEQRES 1 B 6 DT DG DA DT DC DA
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
MODEL 1
Complete list - 25 20 Bytes