Header list of 1dk3.pdb file
Complete list - 16 20 Bytes
HEADER TRANSFERASE 06-DEC-99 1DK3
TITLE REFINED SOLUTION STRUCTURE OF THE N-TERMINAL DOMAIN OF DNA POLYMERASE
TITLE 2 BETA
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: DNA POLYMERASE BETA;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: N-TERMINAL DOMAIN, RESIDUES 1-87;
COMPND 5 EC: 2.7.7.7;
COMPND 6 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS;
SOURCE 3 ORGANISM_COMMON: NORWAY RAT;
SOURCE 4 ORGANISM_TAXID: 10116;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PRSET-8K
KEYWDS DNA-BINDING, DEOXYRIBOSE 5'-PHOSPHATE LYASE, NUCLEOTIDYLTRANSFERASE,
KEYWDS 2 TRANSFERASE
EXPDTA SOLUTION NMR
MDLTYP MINIMIZED AVERAGE
AUTHOR M.W.MACIEJEWSKI,R.PRASAD,D.-J.LIU,S.H.WILSON,G.P.MULLEN
REVDAT 4 16-FEB-22 1DK3 1 REMARK
REVDAT 3 24-FEB-09 1DK3 1 VERSN
REVDAT 2 01-APR-03 1DK3 1 JRNL
REVDAT 1 14-FEB-00 1DK3 0
JRNL AUTH M.W.MACIEJEWSKI,D.LIU,R.PRASAD,S.H.WILSON,G.P.MULLEN
JRNL TITL BACKBONE DYNAMICS AND REFINED SOLUTION STRUCTURE OF THE
JRNL TITL 2 N-TERMINAL DOMAIN OF DNA POLYMERASE BETA. CORRELATION WITH
JRNL TITL 3 DNA BINDING AND DRP LYASE ACTIVITY.
JRNL REF J.MOL.BIOL. V. 296 229 2000
JRNL REFN ISSN 0022-2836
JRNL PMID 10656829
JRNL DOI 10.1006/JMBI.1999.3455
REMARK 1
REMARK 1 REFERENCE 1
REMARK 1 AUTH D.-J.LIU,R.PRASAD,S.H.WILSON,E.F.DEROSE,G.P.MULLEN
REMARK 1 TITL THREE-DIMENSIONAL SOLUTION STRUCTURE OF THE N-TERMINAL
REMARK 1 TITL 2 DOMAIN OF DNA POLYMERASE BETA AND MAPPING OF THE SSDNA
REMARK 1 TITL 3 INTERACTION INTERFACE
REMARK 1 REF BIOCHEMISTRY V. 35 6188 1996
REMARK 1 REFN ISSN 0006-2960
REMARK 1 DOI 10.1021/BI952656O
REMARK 1 REFERENCE 2
REMARK 1 AUTH D.-J.LIU,E.F.DEROSE,R.PRASAD,S.H.WILSON,G.P.MULLEN
REMARK 1 TITL ASSIGNMENTS OF 1H, 15N, AND 13C RESONANCES FOR THE BACKBONE
REMARK 1 TITL 2 AND SIDE CHAINS OF THE N-TERMINAL DOMAIN OF DNA POLYMERASE
REMARK 1 TITL 3 BETA. DETERMINATION OF THE SECONDARY STRUCTURE AND TERTIARY
REMARK 1 TITL 4 CONTACTS.
REMARK 1 REF BIOCHEMISTRY V. 33 9537 1994
REMARK 1 REFN ISSN 0006-2960
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : VNMR 4.3, X-PLOR 4.0
REMARK 3 AUTHORS : VARIAN (VNMR), BRUNGER (X-PLOR)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS:
REMARK 3 THE NMR RESTRAINTS INCLUDED 921 USEFUL NOE DETERMINED UPPER
REMARK 3 DISTANCE
REMARK 3 RESTRAINTS, 41 HYDROGEN BONDS, AND 135 PHI AND CHI TORSION ANGLE
REMARK 3 RESTRAINTS.
REMARK 3 STRUCTURES WERE CALCULATED IN THE PROGRAM DYANA USING TORSION
REMARK 3 ANGLE DYNAMICS.
REMARK 3 THE CALCULATION STARTED WITH 100 RANDOMIZED STRUCTURES. THE 50
REMARK 3 STRUCTURES WITH
REMARK 3 THE LOWEST TARGET FUNCTION WERE THEN REFINED WITHIN XPLOR USING
REMARK 3 SIMULATED
REMARK 3 ANNEALING. THE 25 LOWEST ENERGY STRUCTURAL CONFORMERS WERE
REMARK 3 SELECTED TO
REMARK 3 REPRESENT THE ENSEMBLE.THE 25 REFINED STRUCTURAL CONFORMERS
REMARK 3 DISPLAYED NO NOE
REMARK 3 VIOLATIONS >0.3 ANGSTROMS AND NO DIHEDRAL ANGLE VIOLATIONS >3
REMARK 3 DEGREES. THE
REMARK 3 MINIMIZED AVERAGE STRUCTURE WAS CALCULATED FROM THE MEAN POSITION
REMARK 3 OF THE
REMARK 3 COORDINATES FOR THE 25 STRUCTURAL CONFORMERS AND WAS REFINED BY
REMARK 3 POWELL ENERGY
REMARK 3 MINIMIZATION IN XPLOR USING FULL NMR RESTRAINTS.
REMARK 4
REMARK 4 1DK3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-DEC-99.
REMARK 100 THE DEPOSITION ID IS D_1000010148.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 300; 298
REMARK 210 PH : 6.7; 6.8
REMARK 210 IONIC STRENGTH : 400; 100
REMARK 210 PRESSURE : AMBIENT; AMBIENT
REMARK 210 SAMPLE CONTENTS : 2.8 MM RAT DNA POLYMERASE BETA N
REMARK 210 -TERMINAL DOMAIN (2-87) U-15N,
REMARK 210 13C; 5MM TRIS- D11; 400MM NACL;
REMARK 210 2 MM RAT DNA POLYMERASE BETA N-
REMARK 210 TERMINAL DOMAIN (2-87) U-15N;
REMARK 210 5MM TRIS-D11; 100MM NACL; 4 MM
REMARK 210 RAT DNA POLYMERASE BETA N-
REMARK 210 TERMINAL DOMAIN (2-87) U-15N;
REMARK 210 5MM TRIS-D11; 400MM NACL; 2.8 MM
REMARK 210 RAT DNA POLYMERASE BETA N-
REMARK 210 TERMINAL DOMAIN (2-87) U-15N,13C;
REMARK 210 5MM TRIS- D11; 400MM NACL; 1.4
REMARK 210 MM RAT DNA POLYMERASE BETA N-
REMARK 210 TERMINAL DOMAIN (2-87); 5MM TRIS-
REMARK 210 D11; 400MM NACL
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 3D_15N
REMARK 210 -SEPARATED_NOESY; 3D_13C-
REMARK 210 SEPARATED_NOESY; HMQC-J
REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ
REMARK 210 SPECTROMETER MODEL : GN500; UNITYPLUS
REMARK 210 SPECTROMETER MANUFACTURER : GE; VARIAN
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : FELIX 95, XEASY 1.3.13, DYANA
REMARK 210 1.5
REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS AND
REMARK 210 SIMULATED ANNEALING
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:
REMARK 210 PROTEOLYTIC PROCESSING REMOVES THE N-TERMINAL MET IN A BACTERIAL
REMARK 210 EXPRESSION
REMARK 210 SYSTEM (SEE KUMAR ET AL., (1990) J. BIOL. CHEM. 265, 2124-2131).
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: TORSION ANGLES
REMARK 500
REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)
REMARK 500
REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI-
REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400
REMARK 500
REMARK 500 M RES CSSEQI PSI PHI
REMARK 500 SER A 2 99.50 60.10
REMARK 500 LYS A 3 -40.85 84.83
REMARK 500 LEU A 11 -72.79 -89.60
REMARK 500 ASN A 12 44.28 -104.73
REMARK 500 SER A 30 -70.48 -77.27
REMARK 500 ALA A 32 57.26 -150.81
REMARK 500 ALA A 78 -79.46 -61.80
REMARK 500 ARG A 83 -179.31 -63.43
REMARK 500 LYS A 84 34.78 -98.54
REMARK 500 GLU A 86 34.51 -98.65
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1BNO RELATED DB: PDB
REMARK 900 THIS IS THE PREVIOUS MINIMIZED AVERAGE STRUCTURE.
REMARK 900 RELATED ID: 1BNP RELATED DB: PDB
REMARK 900 THIS IS A PREVIOUS GROUP OF 55 STRUCTURAL CONFORMERS.
DBREF 1DK3 A 1 87 UNP P06766 DPOB_RAT 1 87
SEQRES 1 A 87 MET SER LYS ARG LYS ALA PRO GLN GLU THR LEU ASN GLY
SEQRES 2 A 87 GLY ILE THR ASP MET LEU VAL GLU LEU ALA ASN PHE GLU
SEQRES 3 A 87 LYS ASN VAL SER GLN ALA ILE HIS LYS TYR ASN ALA TYR
SEQRES 4 A 87 ARG LYS ALA ALA SER VAL ILE ALA LYS TYR PRO HIS LYS
SEQRES 5 A 87 ILE LYS SER GLY ALA GLU ALA LYS LYS LEU PRO GLY VAL
SEQRES 6 A 87 GLY THR LYS ILE ALA GLU LYS ILE ASP GLU PHE LEU ALA
SEQRES 7 A 87 THR GLY LYS LEU ARG LYS LEU GLU LYS
HELIX 1 1 GLY A 14 VAL A 29 1 16
HELIX 2 2 ILE A 33 LYS A 48 1 16
HELIX 3 3 SER A 55 LYS A 61 1 7
HELIX 4 4 THR A 67 THR A 79 1 13
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 - 16 20 Bytes