Header list of 1nyd.pdb file
Complete list - 23 20 Bytes
HEADER DNA 12-FEB-03 1NYD
TITLE SOLUTION STRUCTURE OF DNA QUADRUPLEX GCGGTGGAT
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: 5'-D(*GP*CP*GP*GP*TP*GP*GP*AP*T)-3';
COMPND 3 CHAIN: A, B, C, D;
COMPND 4 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES
KEYWDS QUADRUPLEX, PARALLEL QUADRUPLEX, MOLECULAR PROPELLER TOPOLOGY, DOUBLE
KEYWDS 2 CHAIN REVERSAL, DNA
EXPDTA SOLUTION NMR
AUTHOR M.WEBBA DA SILVA
REVDAT 3 23-FEB-22 1NYD 1 REMARK
REVDAT 2 24-FEB-09 1NYD 1 VERSN
REVDAT 1 24-FEB-04 1NYD 0
JRNL AUTH M.WEBBA DA SILVA
JRNL TITL ASSOCIATION OF DNA QUADRUPLEXES THROUGH G:C:G:C TETRADS.
JRNL TITL 2 SOLUTION STRUCTURE OF D(GCGGTGGAT).
JRNL REF BIOCHEMISTRY V. 42 14356 2003
JRNL REFN ISSN 0006-2960
JRNL PMID 14661946
JRNL DOI 10.1021/BI0355185
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : FELIX 1998, X-PLOR 3.1
REMARK 3 AUTHORS : MSI (FELIX), BRUNGER (X-PLOR)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 1NYD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-FEB-03.
REMARK 100 THE DEPOSITION ID IS D_1000018348.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 293; 273
REMARK 210 PH : 6.6; 6.6
REMARK 210 IONIC STRENGTH : 100 MM NACL; 100 MM NACL
REMARK 210 PRESSURE : 1 ATM; 1 ATM
REMARK 210 SAMPLE CONTENTS : 4 MM SAMPLE IN 100 MM NACL, 2 MM
REMARK 210 PHOSPHATE; 4 MM SAMPLE IN 100 MM
REMARK 210 NACL, 2 MM PHOSPHATE
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 2D TOCSY; DQF-COSY;
REMARK 210 (1H,13C)HSQC; (1H,15N)HSQC; JR-
REMARK 210 HMBC
REMARK 210 SPECTROMETER FIELD STRENGTH : 400 MHZ; 500 MHZ; 600 MHZ
REMARK 210 SPECTROMETER MODEL : UNITY; INOVA
REMARK 210 SPECTROMETER MANUFACTURER : VARIAN
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : INSIGHT II 2000
REMARK 210 METHOD USED : DISTANCE GEOMETRY, SIMULATED
REMARK 210 ANNEALING, MOLECULAR DYNAMICS
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: STRUCTURE DETERMINED USING HOMO- AND HETERONUCLEAR
REMARK 210 TECHNIQUES WITH EXPLICIT CORRELATIONS BETWEEN EXCHANGEABLE AND
REMARK 210 NON-EXCHANGEABLE SIGNALS.
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: TETRAMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D
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 DT B 5 C5 DT B 5 C7 0.036
REMARK 500 DG D 4 C6 DG D 4 N1 -0.042
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 1 N9 - C1' - C2' ANGL. DEV. = 8.7 DEGREES
REMARK 500 DG A 1 O4' - C1' - N9 ANGL. DEV. = 6.5 DEGREES
REMARK 500 DC A 2 C4' - C3' - C2' ANGL. DEV. = -4.6 DEGREES
REMARK 500 DC A 2 N1 - C1' - C2' ANGL. DEV. = 11.4 DEGREES
REMARK 500 DC A 2 N1 - C2 - O2 ANGL. DEV. = 4.2 DEGREES
REMARK 500 DC A 2 C3' - O3' - P ANGL. DEV. = 11.6 DEGREES
REMARK 500 DG A 3 C4' - C3' - C2' ANGL. DEV. = -5.1 DEGREES
REMARK 500 DG A 3 O4' - C1' - N9 ANGL. DEV. = 9.2 DEGREES
REMARK 500 DG A 4 C3' - C2' - C1' ANGL. DEV. = -5.6 DEGREES
REMARK 500 DG A 4 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES
REMARK 500 DT A 5 O4' - C1' - C2' ANGL. DEV. = -8.7 DEGREES
REMARK 500 DT A 5 O4' - C1' - N1 ANGL. DEV. = 5.2 DEGREES
REMARK 500 DG A 6 C4' - C3' - C2' ANGL. DEV. = -5.9 DEGREES
REMARK 500 DG A 6 O4' - C1' - C2' ANGL. DEV. = -8.6 DEGREES
REMARK 500 DG A 6 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES
REMARK 500 DG A 7 O4' - C1' - C2' ANGL. DEV. = -5.3 DEGREES
REMARK 500 DG A 7 C3' - O3' - P ANGL. DEV. = 9.3 DEGREES
REMARK 500 DA A 8 C4' - C3' - C2' ANGL. DEV. = -4.5 DEGREES
REMARK 500 DA A 8 C3' - C2' - C1' ANGL. DEV. = -4.9 DEGREES
REMARK 500 DA A 8 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES
REMARK 500 DT A 9 O4' - C4' - C3' ANGL. DEV. = -2.4 DEGREES
REMARK 500 DT A 9 C4' - C3' - C2' ANGL. DEV. = -4.5 DEGREES
REMARK 500 DT A 9 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES
REMARK 500 DT A 9 C6 - C5 - C7 ANGL. DEV. = -5.5 DEGREES
REMARK 500 DG B 1 N9 - C1' - C2' ANGL. DEV. = 8.6 DEGREES
REMARK 500 DG B 1 O4' - C1' - N9 ANGL. DEV. = 6.5 DEGREES
REMARK 500 DC B 2 C4' - C3' - C2' ANGL. DEV. = -4.7 DEGREES
REMARK 500 DC B 2 N1 - C1' - C2' ANGL. DEV. = 11.4 DEGREES
REMARK 500 DC B 2 N1 - C2 - O2 ANGL. DEV. = 4.2 DEGREES
REMARK 500 DC B 2 C3' - O3' - P ANGL. DEV. = 11.6 DEGREES
REMARK 500 DG B 3 C4' - C3' - C2' ANGL. DEV. = -5.0 DEGREES
REMARK 500 DG B 3 O4' - C1' - N9 ANGL. DEV. = 9.2 DEGREES
REMARK 500 DG B 4 C3' - C2' - C1' ANGL. DEV. = -5.8 DEGREES
REMARK 500 DG B 4 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES
REMARK 500 DT B 5 O4' - C1' - C2' ANGL. DEV. = -8.6 DEGREES
REMARK 500 DT B 5 O4' - C1' - N1 ANGL. DEV. = 5.3 DEGREES
REMARK 500 DG B 6 C4' - C3' - C2' ANGL. DEV. = -5.7 DEGREES
REMARK 500 DG B 6 O4' - C1' - C2' ANGL. DEV. = -8.6 DEGREES
REMARK 500 DG B 6 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES
REMARK 500 DG B 7 O4' - C1' - C2' ANGL. DEV. = -5.6 DEGREES
REMARK 500 DG B 7 C3' - O3' - P ANGL. DEV. = 9.3 DEGREES
REMARK 500 DA B 8 C4' - C3' - C2' ANGL. DEV. = -4.4 DEGREES
REMARK 500 DA B 8 C3' - C2' - C1' ANGL. DEV. = -4.9 DEGREES
REMARK 500 DA B 8 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES
REMARK 500 DT B 9 O4' - C4' - C3' ANGL. DEV. = -2.4 DEGREES
REMARK 500 DT B 9 C4' - C3' - C2' ANGL. DEV. = -4.2 DEGREES
REMARK 500 DT B 9 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES
REMARK 500 DT B 9 C6 - C5 - C7 ANGL. DEV. = -5.5 DEGREES
REMARK 500 DG C 1 N9 - C1' - C2' ANGL. DEV. = 8.6 DEGREES
REMARK 500 DG C 1 O4' - C1' - N9 ANGL. DEV. = 6.5 DEGREES
REMARK 500
REMARK 500 THIS ENTRY HAS 96 ANGLE DEVIATIONS.
REMARK 500
REMARK 500 REMARK: NULL
DBREF 1NYD A 1 9 PDB 1NYD 1NYD 1 9
DBREF 1NYD B 1 9 PDB 1NYD 1NYD 1 9
DBREF 1NYD C 1 9 PDB 1NYD 1NYD 1 9
DBREF 1NYD D 1 9 PDB 1NYD 1NYD 1 9
SEQRES 1 A 9 DG DC DG DG DT DG DG DA DT
SEQRES 1 B 9 DG DC DG DG DT DG DG DA DT
SEQRES 1 C 9 DG DC DG DG DT DG DG DA DT
SEQRES 1 D 9 DG DC DG DG DT DG DG DA DT
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 20 Bytes