Header list of 143d.pdb file
Complete list - 29 20 Bytes
HEADER DNA 08-OCT-93 143D
TITLE SOLUTION STRUCTURE OF THE HUMAN TELOMERIC REPEAT D(AG3[T2AG3]3) OF THE
TITLE 2 G-QUADRUPLEX
CAVEAT 143D DG A 3 HAS WRONG CHIRALITY AT ATOM C4' DG A 3 HAS WRONG
CAVEAT 2 143D CHIRALITY AT ATOM C3' DG A 10 HAS WRONG CHIRALITY AT ATOM
CAVEAT 3 143D C3' DT A 11 HAS WRONG CHIRALITY AT ATOM C3' DT A 11 HAS
CAVEAT 4 143D WRONG CHIRALITY AT ATOM C1' DA A 13 HAS WRONG CHIRALITY AT
CAVEAT 5 143D ATOM C3' DG A 2 HAS WRONG CHIRALITY AT ATOM C4' DG A 4 HAS
CAVEAT 6 143D WRONG CHIRALITY AT ATOM C4' DG A 10 HAS WRONG CHIRALITY AT
CAVEAT 7 143D ATOM C4' DA A 1 HAS WRONG CHIRALITY AT ATOM C4' DG A 21 HAS
CAVEAT 8 143D WRONG CHIRALITY AT ATOM C4' DT A 5 HAS WRONG CHIRALITY AT
CAVEAT 9 143D ATOM C1' DT A 6 HAS WRONG CHIRALITY AT ATOM C3' DA A 13 HAS
CAVEAT 10 143D WRONG CHIRALITY AT ATOM C1' DT A 17 HAS WRONG CHIRALITY AT
CAVEAT 11 143D ATOM C1'
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: DNA (5'-
COMPND 3 D(*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*G)-
COMPND 4 3');
COMPND 5 CHAIN: A;
COMPND 6 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT;
SOURCE 4 ORGANISM_TAXID: 32630;
SOURCE 5 OTHER_DETAILS: CHEMICALLY SYNTHESIZED
KEYWDS DNA, HUMAN TELOMERIC SEQUENCE, AG3 REPEAT
EXPDTA SOLUTION NMR
NUMMDL 6
AUTHOR Y.WANG,D.J.PATEL
REVDAT 5 29-MAR-23 143D 1 CAVEAT SOURCE
REVDAT 4 16-FEB-22 143D 1 REMARK
REVDAT 3 24-FEB-09 143D 1 VERSN
REVDAT 2 01-APR-03 143D 1 JRNL
REVDAT 1 30-APR-94 143D 0
JRNL AUTH Y.WANG,D.J.PATEL
JRNL TITL SOLUTION STRUCTURE OF THE HUMAN TELOMERIC REPEAT
JRNL TITL 2 D[AG3(T2AG3)3] G-TETRAPLEX.
JRNL REF STRUCTURE V. 1 263 1993
JRNL REFN ISSN 0969-2126
JRNL PMID 8081740
JRNL DOI 10.1016/0969-2126(93)90015-9
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: A SET OF SIX STRUCTURES WERE OBTAINED
REMARK 3 USING METRIC MATRIX DISTANCE GEOMETRY, AND SUBSEQUENTLY REFINED
REMARK 3 BY DISTANCE-RESTRAINED MOLECULAR DYNAMICS USING A SET OF INTER-
REMARK 3 PROTON DISTANCES AND DIHEDRAL ANGLE RESTRAINTS DERIVED FROM THE
REMARK 3 NMR DATA. THE SIX DISTANCE-REFINED STRUCTURES WERE REFINED
REMARK 3 FURTHER USING RELAXATION-MATRIX BASED NOE INTENSITY-RESTRAINED
REMARK 3 MOLECULAR DYNAMICS. THE FINAL SIX STRUCTURES WERE OBTAINED BY
REMARK 3 TAKING THE AVERAGE COORDINATES OF THE LAST 2 PS OF THE DYNAMICS
REMARK 3 DURING RELAXATION MATRIX REFINEMENT AND MINIMIZED. THE R(1/6)
REMARK 3 VALUE WAS USED TO REFINE THE STRUCTURE DURING RELAXATION MATRIX
REMARK 3 REFINEMENT. THE R(1/6) FACTOR AND THE RMS DEVIATIONS FROM IDEAL
REMARK 3 GEOMETRY FOR THE SIX FINAL STRUCTURES ARE: MODEL1 MODEL2 MODEL3
REMARK 3 MODEL4 MODEL5 MODEL6 R(1/6) FACTOR 0.021 0.016 0.022 0.026 0.024
REMARK 3 0.027 BOND (ANG) 0.009 0.008 0.009 0.011 0.009 0.011 ANGLES (DEG)
REMARK 3 2.949 3.085 3.286 3.853 3.038 3.157 IMPROPERS (DEG) 0.285 0.221
REMARK 3 0.267 0.235 0.243 0.248
REMARK 4
REMARK 4 143D 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_1000170100.
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 : 6
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 6
REMARK 210 CONFORMERS, SELECTION CRITERIA : ALL CALCULATED STRUCTURES
REMARK 210 SUBMITTED
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: MONOMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
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 H62 DA A 7 O2 DT A 18 1.43
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 5 C3' DT A 5 C2' -0.049
REMARK 500 1 DT A 6 C3' DT A 6 C2' 0.086
REMARK 500 1 DT A 6 C5 DT A 6 C7 0.050
REMARK 500 1 DT A 11 C5' DT A 11 C4' 0.042
REMARK 500 1 DT A 12 C5 DT A 12 C7 0.038
REMARK 500 1 DA A 19 C5' DA A 19 C4' 0.048
REMARK 500 2 DT A 5 C6 DT A 5 N1 -0.052
REMARK 500 2 DT A 5 C5 DT A 5 C7 0.038
REMARK 500 2 DT A 6 C5 DT A 6 C7 0.037
REMARK 500 2 DA A 13 C5' DA A 13 C4' 0.048
REMARK 500 2 DT A 17 C5 DT A 17 C7 0.037
REMARK 500 2 DT A 18 C5 DT A 18 C7 0.039
REMARK 500 2 DA A 19 C5' DA A 19 C4' 0.042
REMARK 500 3 DA A 1 C5' DA A 1 C4' 0.046
REMARK 500 3 DT A 5 C6 DT A 5 N1 -0.053
REMARK 500 3 DT A 5 C5 DT A 5 C7 0.041
REMARK 500 3 DT A 6 C3' DT A 6 C2' 0.086
REMARK 500 3 DT A 6 C5 DT A 6 C7 0.036
REMARK 500 3 DT A 12 C5 DT A 12 C7 0.042
REMARK 500 3 DT A 17 C5 DT A 17 C7 0.036
REMARK 500 4 DT A 5 C5 DT A 5 C7 0.036
REMARK 500 4 DT A 6 C3' DT A 6 C2' 0.093
REMARK 500 4 DG A 9 C2' DG A 9 C1' 0.064
REMARK 500 4 DT A 12 C2' DT A 12 C1' 0.088
REMARK 500 4 DA A 13 C5' DA A 13 C4' 0.051
REMARK 500 4 DT A 18 C5 DT A 18 C7 0.037
REMARK 500 4 DA A 19 C5' DA A 19 C4' 0.048
REMARK 500 5 DT A 5 C5 DT A 5 C7 0.037
REMARK 500 5 DT A 6 C5 DT A 6 C7 0.048
REMARK 500 5 DT A 11 C5 DT A 11 C7 0.038
REMARK 500 5 DT A 12 C5 DT A 12 C7 0.037
REMARK 500 5 DA A 19 C5' DA A 19 C4' 0.043
REMARK 500 6 DA A 1 C5' DA A 1 C4' 0.043
REMARK 500 6 DT A 5 C6 DT A 5 N1 -0.048
REMARK 500 6 DT A 6 C3' DT A 6 C2' 0.092
REMARK 500 6 DT A 6 C5 DT A 6 C7 0.036
REMARK 500 6 DG A 9 C2' DG A 9 C1' 0.060
REMARK 500 6 DT A 11 C2' DT A 11 C1' 0.067
REMARK 500 6 DT A 12 C5 DT A 12 C7 0.041
REMARK 500 6 DA A 13 C5' DA A 13 C4' 0.050
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 DA A 1 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES
REMARK 500 1 DG A 3 O4' - C4' - C3' ANGL. DEV. = 3.7 DEGREES
REMARK 500 1 DG A 3 C5' - C4' - O4' ANGL. DEV. = -21.1 DEGREES
REMARK 500 1 DG A 3 C2' - C3' - O3' ANGL. DEV. = -24.0 DEGREES
REMARK 500 1 DG A 3 C4' - C3' - C2' ANGL. DEV. = -5.2 DEGREES
REMARK 500 1 DG A 3 N9 - C1' - C2' ANGL. DEV. = 9.5 DEGREES
REMARK 500 1 DG A 3 O4' - C1' - N9 ANGL. DEV. = 4.6 DEGREES
REMARK 500 1 DG A 4 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES
REMARK 500 1 DT A 5 O4' - C1' - N1 ANGL. DEV. = 5.4 DEGREES
REMARK 500 1 DT A 5 C6 - C5 - C7 ANGL. DEV. = -5.8 DEGREES
REMARK 500 1 DT A 6 C3' - C2' - C1' ANGL. DEV. = -5.7 DEGREES
REMARK 500 1 DT A 6 O4' - C1' - C2' ANGL. DEV. = -5.1 DEGREES
REMARK 500 1 DA A 7 C3' - C2' - C1' ANGL. DEV. = -5.6 DEGREES
REMARK 500 1 DA A 7 O4' - C1' - N9 ANGL. DEV. = 6.4 DEGREES
REMARK 500 1 DG A 8 C3' - O3' - P ANGL. DEV. = 8.5 DEGREES
REMARK 500 1 DG A 9 C3' - C2' - C1' ANGL. DEV. = -5.6 DEGREES
REMARK 500 1 DG A 9 O4' - C1' - C2' ANGL. DEV. = -6.3 DEGREES
REMARK 500 1 DT A 12 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES
REMARK 500 1 DG A 16 C3' - C2' - C1' ANGL. DEV. = -5.0 DEGREES
REMARK 500 1 DG A 16 O4' - C1' - N9 ANGL. DEV. = 5.7 DEGREES
REMARK 500 1 DT A 17 C3' - C2' - C1' ANGL. DEV. = -6.1 DEGREES
REMARK 500 1 DT A 17 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES
REMARK 500 1 DG A 20 C3' - C2' - C1' ANGL. DEV. = -6.1 DEGREES
REMARK 500 1 DG A 20 C3' - O3' - P ANGL. DEV. = 9.2 DEGREES
REMARK 500 1 DG A 21 C3' - C2' - C1' ANGL. DEV. = -6.1 DEGREES
REMARK 500 1 DG A 21 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES
REMARK 500 2 DA A 1 C3' - O3' - P ANGL. DEV. = 9.9 DEGREES
REMARK 500 2 DG A 2 C3' - C2' - C1' ANGL. DEV. = -5.2 DEGREES
REMARK 500 2 DG A 2 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES
REMARK 500 2 DG A 3 O4' - C4' - C3' ANGL. DEV. = -4.2 DEGREES
REMARK 500 2 DG A 3 C4' - C3' - O3' ANGL. DEV. = 18.6 DEGREES
REMARK 500 2 DG A 3 O4' - C1' - N9 ANGL. DEV. = 5.5 DEGREES
REMARK 500 2 DG A 4 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES
REMARK 500 2 DT A 5 O4' - C1' - N1 ANGL. DEV. = 3.6 DEGREES
REMARK 500 2 DT A 6 C4' - C3' - C2' ANGL. DEV. = -5.5 DEGREES
REMARK 500 2 DT A 6 C3' - C2' - C1' ANGL. DEV. = -5.8 DEGREES
REMARK 500 2 DT A 6 O4' - C1' - C2' ANGL. DEV. = -6.1 DEGREES
REMARK 500 2 DT A 6 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES
REMARK 500 2 DA A 7 C5' - C4' - O4' ANGL. DEV. = 8.0 DEGREES
REMARK 500 2 DA A 7 C1' - O4' - C4' ANGL. DEV. = -6.3 DEGREES
REMARK 500 2 DA A 7 C3' - C2' - C1' ANGL. DEV. = -5.8 DEGREES
REMARK 500 2 DA A 7 O4' - C1' - C2' ANGL. DEV. = -5.9 DEGREES
REMARK 500 2 DA A 7 O4' - C1' - N9 ANGL. DEV. = 8.5 DEGREES
REMARK 500 2 DG A 9 C3' - O3' - P ANGL. DEV. = 11.5 DEGREES
REMARK 500 2 DG A 10 O4' - C1' - N9 ANGL. DEV. = 10.7 DEGREES
REMARK 500 2 DT A 11 C4' - C3' - C2' ANGL. DEV. = -5.9 DEGREES
REMARK 500 2 DT A 11 C3' - C2' - C1' ANGL. DEV. = -6.1 DEGREES
REMARK 500 2 DT A 11 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES
REMARK 500 2 DT A 12 O4' - C1' - N1 ANGL. DEV. = 5.2 DEGREES
REMARK 500 2 DT A 12 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES
REMARK 500
REMARK 500 THIS ENTRY HAS 216 ANGLE DEVIATIONS.
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 201D RELATED DB: PDB
REMARK 900 ENSEMBLE OF 6 STRUCTURES
REMARK 900 RELATED ID: 179D RELATED DB: PDB
REMARK 900 RELATED ID: 186D RELATED DB: PDB
DBREF 143D A 1 22 PDB 143D 143D 1 22
SEQRES 1 A 22 DA DG DG DG DT DT DA DG DG DG DT DT DA
SEQRES 2 A 22 DG DG DG DT DT DA DG DG DG
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 - 29 20 Bytes