Header list of 139d.pdb file
Complete list - 16 20 Bytes
HEADER DNA 28-SEP-93 139D
TITLE SOLUTION STRUCTURE OF A PARALLEL-STRANDED G-QUADRUPLEX DNA
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: DNA (5'-D(*TP*TP*GP*GP*GP*GP*T)-3');
COMPND 3 CHAIN: A, B, C, D;
COMPND 4 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 OTHER_DETAILS: CHEMICALLY SYNTHESIZED
KEYWDS DNA, G-QUADRUPLEX, ANTI GLYCOSIDIC TORSION ANGLES
EXPDTA SOLUTION NMR
NUMMDL 4
AUTHOR D.J.PATEL,Y.WANG
REVDAT 4 16-FEB-22 139D 1 REMARK
REVDAT 3 07-APR-09 139D 1 REMARK
REVDAT 2 24-FEB-09 139D 1 VERSN
REVDAT 1 31-JAN-94 139D 0
JRNL AUTH Y.WANG,D.J.PATEL
JRNL TITL SOLUTION STRUCTURE OF A PARALLEL-STRANDED G-QUADRUPLEX DNA.
JRNL REF J.MOL.BIOL. V. 234 1171 1993
JRNL REFN ISSN 0022-2836
JRNL PMID 8263919
JRNL DOI 10.1006/JMBI.1993.1668
REMARK 1
REMARK 1 REFERENCE 1
REMARK 1 AUTH Y.WANG,D.J.PATEL
REMARK 1 TITL GUANINE RESIDUES IN D(T2AG3) AND D(T2G4) FORM
REMARK 1 TITL 2 PARALLEL-STRANDED POTASSIUM CATION STABILIZED G-QUADRUPLEXES
REMARK 1 TITL 3 WITH ANTI GLYCOSIDIC TORSION ANGLES IN SOLUTION
REMARK 1 REF BIOCHEMISTRY V. 31 8112 1992
REMARK 1 REFN ISSN 0006-2960
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : X-PLOR
REMARK 3 AUTHORS : BRUNGER
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: RESTRAINED MOLECULAR DYNAMICS
REMARK 3 CALCULATIONS WERE DONE ON A MOLECULAR MODEL BUILT TO
REMARK 3 QUALITATIVELY FIT THE NMR DATA. THE REFINEMENT WAS CONDUCTED IN
REMARK 3 TWO STAGES. IN THE FIRST STAGE, SEVEN STRUCTURES WERE CALCULATED
REMARK 3 USING DISTANCE RESTRAINTS (WITH DIFFERENT SEEDS FOR INITIAL
REMARK 3 VELOCITY ASSIGNMENTS). IN THE SECOND STAGE, FOUR OF THE SEVEN
REMARK 3 DISTANCE-REFINED STRUCTURES WERE REFINED FURTHER BY NOE
REMARK 3 INTENSITY-RESTRAINED MOLECULAR DYNAMICS CALCULATIONS. THE R(1/6)
REMARK 3 VALUE WAS USED TO MONITOR THE REFINEMENT DURING THE SECOND
REMARK 3 STAGE. THE FINAL R(1/6) VALUES FOR THE FOUR AVERAGED MINIMIZED
REMARK 3 STRUCTURES WERE BETWEEN 0.025 AND 0.033. RMS DEVIATIONS FROM
REMARK 3 IDEALIZED GEOMETRY FOR THE TWO AVERAGED MINIMIZED STRUCTURES ARE
REMARK 3 AS FOLLOWS: MODEL1 MODEL2 MODEL3 MODEL4 BOND (ANGSTROMS) 0.013
REMARK 3 0.013 0.012 0.011 ANGLES (DEGREES) 2.713 2.634 2.731 2.728
REMARK 3 IMPROPERS (DEGREES) 0.476 0.560 0.242 0.280. THE STRUCTURE HAS
REMARK 3 AN APPROXIMATE FOUR-FOLD SYMMETRY RELATING THE FOUR STRANDS WITH
REMARK 3 THE SYMMETRY AXIS COINCIDENT WITH THE HELICAL AXIS. THE
REMARK 3 TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD
REMARK 3 APPROXIMATE COORDINATES FOR CHAIN *B* WHEN APPLIED TO CHAIN *A*.
REMARK 3 IT WILL ALSO YIELD APPROXIMATE COORDINATES FOR CHAIN *C* WHEN
REMARK 3 APPLIED TO CHAIN *B* AND WILL YIELD APPROXIMATE COORDINATES FOR
REMARK 3 CHAIN *D* WHEN APPLIED TO CHAIN *C*.
REMARK 4
REMARK 4 139D COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.
REMARK 100 THE DEPOSITION ID IS D_1000170090.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : NULL
REMARK 210 PH : NULL
REMARK 210 IONIC STRENGTH : NULL
REMARK 210 PRESSURE : NULL
REMARK 210 SAMPLE CONTENTS : NULL
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL
REMARK 210 SPECTROMETER FIELD STRENGTH : NULL
REMARK 210 SPECTROMETER MODEL : NULL
REMARK 210 SPECTROMETER MANUFACTURER : NULL
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : NULL
REMARK 210 METHOD USED : DISTANCE GEOMETRY, MOLECULAR
REMARK 210 DYNAMICS
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 7
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 4
REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST
REMARK 210 RESTRAINT VIOLATIONS,STRUCTURES
REMARK 210 WITH THE LOWEST ENERGY
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL
REMARK 210
REMARK 210 REMARK: NULL
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: 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 O4 DT A 7 HO3' DT B 7 1.58
REMARK 500 O4 DT B 7 HO3' DT C 7 1.59
REMARK 500 O4 DT C 7 HO3' DT D 7 1.59
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 1 DT A 1 C5' DT A 1 C4' 0.064
REMARK 500 1 DT A 7 C4' DT A 7 C3' 0.067
REMARK 500 1 DT B 1 C5' DT B 1 C4' 0.059
REMARK 500 1 DT B 7 C5' DT B 7 C4' 0.043
REMARK 500 1 DT B 7 C4' DT B 7 C3' 0.061
REMARK 500 1 DT C 1 C5' DT C 1 C4' 0.063
REMARK 500 1 DT C 1 C5 DT C 1 C7 0.037
REMARK 500 1 DT C 2 C5' DT C 2 C4' 0.048
REMARK 500 1 DT C 7 C5' DT C 7 C4' 0.057
REMARK 500 1 DT C 7 C4' DT C 7 C3' 0.080
REMARK 500 1 DT C 7 C5 DT C 7 C7 0.041
REMARK 500 1 DT D 1 C5' DT D 1 C4' 0.075
REMARK 500 1 DT D 1 C4' DT D 1 C3' 0.065
REMARK 500 1 DT D 7 C5' DT D 7 C4' 0.057
REMARK 500 1 DT D 7 C4' DT D 7 C3' 0.073
REMARK 500 2 DT A 2 C5 DT A 2 C7 0.048
REMARK 500 2 DG A 6 C6 DG A 6 N1 -0.044
REMARK 500 2 DT B 7 C5' DT B 7 C4' 0.048
REMARK 500 2 DT B 7 C5 DT B 7 C7 0.050
REMARK 500 2 DT C 1 C5' DT C 1 C4' 0.067
REMARK 500 2 DT C 1 C5 DT C 1 C7 0.048
REMARK 500 2 DT D 1 C5 DT D 1 C7 0.040
REMARK 500 2 DT D 7 C5' DT D 7 C4' 0.053
REMARK 500 3 DT A 1 C5' DT A 1 C4' 0.083
REMARK 500 3 DT A 1 C5 DT A 1 C7 0.039
REMARK 500 3 DT A 2 C5 DT A 2 C7 0.038
REMARK 500 3 DT A 7 C5' DT A 7 C4' 0.048
REMARK 500 3 DT A 7 C4' DT A 7 C3' 0.064
REMARK 500 3 DT B 1 C5' DT B 1 C4' 0.083
REMARK 500 3 DT B 1 C5 DT B 1 C7 0.041
REMARK 500 3 DT B 2 C5 DT B 2 C7 0.039
REMARK 500 3 DT B 7 C5' DT B 7 C4' 0.048
REMARK 500 3 DT B 7 C4' DT B 7 C3' 0.064
REMARK 500 3 DT C 1 C5' DT C 1 C4' 0.083
REMARK 500 3 DT C 1 C5 DT C 1 C7 0.041
REMARK 500 3 DT C 2 C5 DT C 2 C7 0.038
REMARK 500 3 DT C 7 C5' DT C 7 C4' 0.047
REMARK 500 3 DT C 7 C4' DT C 7 C3' 0.066
REMARK 500 3 DT D 1 C5' DT D 1 C4' 0.083
REMARK 500 3 DT D 1 C5 DT D 1 C7 0.039
REMARK 500 3 DT D 2 C5 DT D 2 C7 0.038
REMARK 500 3 DT D 7 C5' DT D 7 C4' 0.046
REMARK 500 3 DT D 7 C4' DT D 7 C3' 0.065
REMARK 500 4 DT A 1 C5' DT A 1 C4' 0.078
REMARK 500 4 DT A 1 C5 DT A 1 C7 0.036
REMARK 500 4 DT A 2 C5 DT A 2 C7 0.038
REMARK 500 4 DT A 7 C5 DT A 7 C7 0.040
REMARK 500 4 DT B 1 C5' DT B 1 C4' 0.079
REMARK 500 4 DT B 2 C5 DT B 2 C7 0.036
REMARK 500 4 DT B 7 C5 DT B 7 C7 0.040
REMARK 500
REMARK 500 THIS ENTRY HAS 58 BOND DEVIATIONS.
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 O4' - C1' - N1 ANGL. DEV. = 5.2 DEGREES
REMARK 500 1 DT A 2 C6 - C5 - C7 ANGL. DEV. = -4.8 DEGREES
REMARK 500 1 DG A 3 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES
REMARK 500 1 DG A 4 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES
REMARK 500 1 DG A 5 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES
REMARK 500 1 DG A 6 C4' - C3' - C2' ANGL. DEV. = -4.7 DEGREES
REMARK 500 1 DG A 6 O4' - C1' - N9 ANGL. DEV. = 10.3 DEGREES
REMARK 500 1 DT A 7 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES
REMARK 500 1 DT B 1 O4' - C4' - C3' ANGL. DEV. = -2.6 DEGREES
REMARK 500 1 DT B 1 O4' - C1' - C2' ANGL. DEV. = -5.3 DEGREES
REMARK 500 1 DT B 1 O4' - C1' - N1 ANGL. DEV. = 7.6 DEGREES
REMARK 500 1 DT B 2 C6 - C5 - C7 ANGL. DEV. = -5.2 DEGREES
REMARK 500 1 DG B 4 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES
REMARK 500 1 DG B 6 C4' - C3' - C2' ANGL. DEV. = -4.3 DEGREES
REMARK 500 1 DG B 6 O4' - C1' - N9 ANGL. DEV. = 9.4 DEGREES
REMARK 500 1 DT B 7 O4' - C4' - C3' ANGL. DEV. = -3.0 DEGREES
REMARK 500 1 DT B 7 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES
REMARK 500 1 DT B 7 C6 - C5 - C7 ANGL. DEV. = -4.2 DEGREES
REMARK 500 1 DT C 1 O4' - C1' - N1 ANGL. DEV. = 7.3 DEGREES
REMARK 500 1 DT C 2 C6 - C5 - C7 ANGL. DEV. = -4.0 DEGREES
REMARK 500 1 DG C 3 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES
REMARK 500 1 DG C 4 O4' - C1' - N9 ANGL. DEV. = 4.1 DEGREES
REMARK 500 1 DG C 6 C4' - C3' - C2' ANGL. DEV. = -4.5 DEGREES
REMARK 500 1 DG C 6 O4' - C1' - N9 ANGL. DEV. = 9.9 DEGREES
REMARK 500 1 DT C 7 O4' - C4' - C3' ANGL. DEV. = -2.5 DEGREES
REMARK 500 1 DT C 7 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES
REMARK 500 1 DT C 7 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES
REMARK 500 1 DT D 1 O4' - C1' - N1 ANGL. DEV. = 6.7 DEGREES
REMARK 500 1 DT D 2 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES
REMARK 500 1 DG D 3 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES
REMARK 500 1 DG D 4 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES
REMARK 500 1 DG D 6 C4' - C3' - C2' ANGL. DEV. = -4.7 DEGREES
REMARK 500 1 DG D 6 O4' - C1' - N9 ANGL. DEV. = 9.3 DEGREES
REMARK 500 1 DT D 7 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES
REMARK 500 1 DT D 7 C6 - C5 - C7 ANGL. DEV. = -4.1 DEGREES
REMARK 500 2 DT A 1 C4 - C5 - C6 ANGL. DEV. = 4.8 DEGREES
REMARK 500 2 DT A 1 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES
REMARK 500 2 DT A 2 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES
REMARK 500 2 DG A 6 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES
REMARK 500 2 DT A 7 C3' - C2' - C1' ANGL. DEV. = -5.3 DEGREES
REMARK 500 2 DT A 7 O4' - C1' - N1 ANGL. DEV. = 8.0 DEGREES
REMARK 500 2 DT B 1 C6 - C5 - C7 ANGL. DEV. = -4.4 DEGREES
REMARK 500 2 DT B 2 N3 - C2 - O2 ANGL. DEV. = -4.6 DEGREES
REMARK 500 2 DG B 6 O4' - C1' - N9 ANGL. DEV. = 3.7 DEGREES
REMARK 500 2 DG B 6 C5 - C6 - N1 ANGL. DEV. = 3.0 DEGREES
REMARK 500 2 DT B 7 O4' - C4' - C3' ANGL. DEV. = -2.6 DEGREES
REMARK 500 2 DT B 7 C3' - C2' - C1' ANGL. DEV. = -5.2 DEGREES
REMARK 500 2 DT B 7 O4' - C1' - N1 ANGL. DEV. = 7.1 DEGREES
REMARK 500 2 DT B 7 C6 - C5 - C7 ANGL. DEV. = -4.9 DEGREES
REMARK 500 2 DT C 1 C4 - C5 - C6 ANGL. DEV. = 4.1 DEGREES
REMARK 500
REMARK 500 THIS ENTRY HAS 112 ANGLE DEVIATIONS.
REMARK 500
REMARK 500 REMARK: NULL
DBREF 139D A 1 7 PDB 139D 139D 1 7
DBREF 139D B 1 7 PDB 139D 139D 1 7
DBREF 139D C 1 7 PDB 139D 139D 1 7
DBREF 139D D 1 7 PDB 139D 139D 1 7
SEQRES 1 A 7 DT DT DG DG DG DG DT
SEQRES 1 B 7 DT DT DG DG DG DG DT
SEQRES 1 C 7 DT DT DG DG DG DG DT
SEQRES 1 D 7 DT DT DG DG DG DG 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
MODEL 1
Complete list - 16 20 Bytes