10 20 30 40 50 60 70 80 1DK3 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER TRANSFERASE 06-DEC-99 1DK3
TITLE REFINED SOLUTION STRUCTURE OF THE N-TERMINAL DOMAIN OF DNA TITLE 2 POLYMERASE 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, KEYWDS 2 NUCLEOTIDYLTRANSFERASE
EXPDTA SOLUTION NMR
MDLTYP MINIMIZED AVERAGE
AUTHOR M.W.MACIEJEWSKI,R.PRASAD,D.-J.LIU,S.H.WILSON,G.P.MULLEN
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, JRNL AUTH 2 G.P.MULLEN JRNL TITL BACKBONE DYNAMICS AND REFINED SOLUTION STRUCTURE JRNL TITL 2 OF THE N-TERMINAL DOMAIN OF DNA POLYMERASE BETA. JRNL TITL 3 CORRELATION WITH DNA BINDING AND DRP LYASE JRNL TITL 4 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 REMARK 1 TITL 2 N-TERMINAL DOMAIN OF DNA POLYMERASE BETA AND REMARK 1 TITL 3 MAPPING OF THE SSDNA 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 REMARK 1 TITL 2 BACKBONE AND SIDE CHAINS OF THE N-TERMINAL DOMAIN REMARK 1 TITL 3 OF DNA POLYMERASE BETA. DETERMINATION OF THE REMARK 1 TITL 4 SECONDARY STRUCTURE AND TERTIARY 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 : X-PLOR 4.0 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE NMR RESTRAINTS INCLUDED 921 REMARK 3 USEFUL NOE DETERMINED UPPER DISTANCE RESTRAINTS, 41 HYDROGEN REMARK 3 BONDS, AND 135 PHI AND CHI TORSION ANGLE RESTRAINTS. REMARK 3 STRUCTURES WERE CALCULATED IN THE PROGRAM DYANA USING TORSION REMARK 3 ANGLE DYNAMICS. THE CALCULATION STARTED WITH 100 RANDOMIZED REMARK 3 STRUCTURES. THE 50 STRUCTURES WITH THE LOWEST TARGET FUNCTION REMARK 3 WERE THEN REFINED WITHIN XPLOR USING SIMULATED ANNEALING. THE REMARK 3 25 LOWEST ENERGY STRUCTURAL CONFORMERS WERE SELECTED TO REMARK 3 REPRESENT THE ENSEMBLE.THE 25 REFINED STRUCTURAL CONFORMERS REMARK 3 DISPLAYED NO NOE VIOLATIONS >0.3 ANGSTROMS AND NO DIHEDRAL REMARK 3 ANGLE VIOLATIONS >3 DEGREES. THE MINIMIZED AVERAGE STRUCTURE REMARK 3 WAS CALCULATED FROM THE MEAN POSITION OF THE COORDINATES FOR REMARK 3 THE 25 STRUCTURAL CONFORMERS AND WAS REFINED BY POWELL ENERGY REMARK 3 MINIMIZATION IN XPLOR USING FULL NMR RESTRAINTS.
REMARK 4 REMARK 4 1DK3 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-DEC-99. REMARK 100 THE RCSB ID CODE IS RCSB010148.
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 REMARK 210 BETA N-TERMINAL DOMAIN (2-87) REMARK 210 U-15N,13C; 5MM TRIS- D11; REMARK 210 400MM NACL; 2 MM RAT DNA REMARK 210 POLYMERASE BETA N-TERMINAL REMARK 210 DOMAIN (2-87) U-15N; 5MM TRIS- REMARK 210 D11; 100MM NACL; 4 MM RAT DNA REMARK 210 POLYMERASE BETA N-TERMINAL REMARK 210 DOMAIN (2-87) U-15N; 5MM TRIS- REMARK 210 D11; 400MM NACL; 2.8 MM RAT REMARK 210 DNA POLYMERASE BETA N-TERMINAL REMARK 210 DOMAIN (2-87) U-15N,13C; 5MM REMARK 210 TRIS- D11; 400MM NACL; 1.4 MM REMARK 210 RAT DNA POLYMERASE BETA N- REMARK 210 TERMINAL DOMAIN (2-87); 5MM REMARK 210 TRIS-D11; 400MM NACL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY, 3D_15N-SEPARATED_ REMARK 210 NOESY, 3D_13C-SEPARATED_NOESY, REMARK 210 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 : VNMR 4.3, FELIX 95, XEASY REMARK 210 1.3.13, DYANA 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: PROTEOLYTIC PROCESSING REMOVES THE N-TERMINAL MET IN A REMARK 210 BACTERIAL EXPRESSION SYSTEM (SEE KUMAR ET AL., (1990) J. BIOL. REMARK 210 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 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