Header list of 1ekw.pdb file
Complete list - 25 201 Bytes
HEADER DNA 09-MAR-00 1EKW
TITLE NMR STRUCTURE OF A DNA THREE-WAY JUNCTION
CAVEAT 1EKW CHIRALLY INCORRECT C4' OF G 31 CHAIN R
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: DNA (5'-D(*GP*CP*TP*GP*CP*CP*AP*CP*CP*G)-3');
COMPND 3 CHAIN: X;
COMPND 4 ENGINEERED: YES;
COMPND 5 MOL_ID: 2;
COMPND 6 MOLECULE: DNA (5'-D(*CP*GP*GP*TP*GP*CP*GP*TP*CP*C)-3');
COMPND 7 CHAIN: H;
COMPND 8 ENGINEERED: YES;
COMPND 9 MOL_ID: 3;
COMPND 10 MOLECULE: DNA (5'-D(*GP*GP*AP*CP*GP*TP*CP*GP*CP*AP*GP*C)-3');
COMPND 11 CHAIN: R;
COMPND 12 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 MOL_ID: 2;
SOURCE 4 SYNTHETIC: YES;
SOURCE 5 MOL_ID: 3;
SOURCE 6 SYNTHETIC: YES
KEYWDS THREE-WAY-JUNCTION, UNPAIRED BASES, DNA
EXPDTA SOLUTION NMR
MDLTYP MINIMIZED AVERAGE
AUTHOR V.THIVIYANATHAN,B.A.LUXON,N.B.LEONTIS,D.DONNE,D.G.GORENSTEIN
REVDAT 4 28-DEC-11 1EKW 1 CAVEAT VERSN
REVDAT 3 24-FEB-09 1EKW 1 VERSN
REVDAT 2 01-APR-03 1EKW 1 JRNL
REVDAT 1 20-MAR-00 1EKW 0
JRNL AUTH V.THIVIYANATHAN,B.A.LUXON,N.B.LEONTIS,N.ILLANGASEKARE,
JRNL AUTH 2 D.G.DONNE,D.G.GORENSTEIN
JRNL TITL HYBRID-HYBRID MATRIX STRUCTURAL REFINEMENT OF A DNA
JRNL TITL 2 THREE-WAY JUNCTION FROM 3D NOESY-NOESY.
JRNL REF J.BIOMOL.NMR V. 14 209 1999
JRNL REFN ISSN 0925-2738
JRNL PMID 10481274
JRNL DOI 10.1023/A:1008330011425
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : NULL
REMARK 3 AUTHORS : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: PARTICLE MESH EWALD METHODS WERE USED.
REMARK 4
REMARK 4 1EKW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-MAR-00.
REMARK 100 THE RCSB ID CODE IS RCSB010688.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 301
REMARK 210 PH : 6.8
REMARK 210 IONIC STRENGTH : 100 MM
REMARK 210 PRESSURE : 1 ATM
REMARK 210 SAMPLE CONTENTS : 2 MM DNA, 0.5MM EDTA, 100 MM
REMARK 210 SODIUM PHOSPHATE, 10 MM MGCL2,
REMARK 210 100MM NACL
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 3D NOESY-NOESY
REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 750 MHZ
REMARK 210 SPECTROMETER MODEL : UNITYPLUS
REMARK 210 SPECTROMETER MANUFACTURER : VARIAN
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : MORASS 2.5
REMARK 210 METHOD USED : COMPLETE RELAXATION MATRIX
REMARK 210 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 : 1
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: TRIMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: X, H, R
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 X 3 C6 DT X 3 N1 -0.044
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 DC X 2 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES
REMARK 500 DT X 3 O4' - C4' - C3' ANGL. DEV. = 6.8 DEGREES
REMARK 500 DT X 3 C4' - C3' - C2' ANGL. DEV. = -5.7 DEGREES
REMARK 500 DT X 3 C4 - C5 - C7 ANGL. DEV. = 4.8 DEGREES
REMARK 500 DT X 3 C6 - C5 - C7 ANGL. DEV. = -9.7 DEGREES
REMARK 500 DT X 3 C6 - N1 - C1' ANGL. DEV. = -9.9 DEGREES
REMARK 500 DG X 4 O4' - C1' - N9 ANGL. DEV. = 9.4 DEGREES
REMARK 500 DC X 6 C4' - C3' - C2' ANGL. DEV. = -7.9 DEGREES
REMARK 500 DC X 6 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES
REMARK 500 DA X 7 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES
REMARK 500 DC X 8 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES
REMARK 500 DC X 9 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES
REMARK 500 DC X 9 C6 - N1 - C1' ANGL. DEV. = -7.5 DEGREES
REMARK 500 DG X 10 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES
REMARK 500 DC H 11 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES
REMARK 500 DG H 12 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES
REMARK 500 DG H 13 C4' - C3' - C2' ANGL. DEV. = -5.2 DEGREES
REMARK 500 DG H 13 O4' - C1' - N9 ANGL. DEV. = 5.8 DEGREES
REMARK 500 DC H 16 O4' - C4' - C3' ANGL. DEV. = 4.7 DEGREES
REMARK 500 DC H 16 N1 - C2 - O2 ANGL. DEV. = 3.8 DEGREES
REMARK 500 DG H 17 N7 - C8 - N9 ANGL. DEV. = 3.2 DEGREES
REMARK 500 DT H 18 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES
REMARK 500 DC H 19 N1 - C2 - O2 ANGL. DEV. = 3.8 DEGREES
REMARK 500 DC H 20 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES
REMARK 500 DG R 22 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES
REMARK 500 DC R 24 O4' - C1' - C2' ANGL. DEV. = -5.3 DEGREES
REMARK 500 DC R 24 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES
REMARK 500 DC R 24 N1 - C2 - O2 ANGL. DEV. = 4.0 DEGREES
REMARK 500 DG R 25 O4' - C1' - C2' ANGL. DEV. = -5.0 DEGREES
REMARK 500 DG R 25 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES
REMARK 500 DT R 26 O4' - C1' - N1 ANGL. DEV. = 6.0 DEGREES
REMARK 500 DC R 27 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES
REMARK 500 DG R 28 O4' - C1' - N9 ANGL. DEV. = 4.7 DEGREES
REMARK 500 DA R 30 O4' - C1' - N9 ANGL. DEV. = 6.0 DEGREES
REMARK 500 DG R 31 C4' - C3' - C2' ANGL. DEV. = -5.7 DEGREES
REMARK 500 DC R 32 C5' - C4' - O4' ANGL. DEV. = 6.9 DEGREES
REMARK 500 DC R 32 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES
REMARK 500 DC R 32 N1 - C2 - O2 ANGL. DEV. = 4.2 DEGREES
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 DG X 1 0.09 SIDE CHAIN
REMARK 500 DT X 3 0.20 SIDE CHAIN
REMARK 500 DC X 5 0.12 SIDE CHAIN
REMARK 500 DC X 6 0.13 SIDE CHAIN
REMARK 500 DA X 7 0.10 SIDE CHAIN
REMARK 500 DC X 9 0.11 SIDE CHAIN
REMARK 500 DG X 10 0.12 SIDE CHAIN
REMARK 500 DG H 13 0.09 SIDE CHAIN
REMARK 500 DG H 15 0.14 SIDE CHAIN
REMARK 500 DC H 16 0.13 SIDE CHAIN
REMARK 500 DC H 19 0.09 SIDE CHAIN
REMARK 500 DG R 22 0.09 SIDE CHAIN
REMARK 500 DG R 25 0.12 SIDE CHAIN
REMARK 500 DG R 28 0.07 SIDE CHAIN
REMARK 500 DG R 31 0.20 SIDE CHAIN
REMARK 500 DC R 32 0.07 SIDE CHAIN
REMARK 500
REMARK 500 REMARK: NULL
DBREF 1EKW X 1 10 PDB 1EKW 1EKW 1 10
DBREF 1EKW H 11 20 PDB 1EKW 1EKW 11 20
DBREF 1EKW R 21 32 PDB 1EKW 1EKW 21 32
SEQRES 1 X 10 DG DC DT DG DC DC DA DC DC DG
SEQRES 1 H 10 DC DG DG DT DG DC DG DT DC DC
SEQRES 1 R 12 DG DG DA DC DG DT DC DG DC DA DG DC
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 - 25 201 Bytes