PDB Short entry for 1NZP HEADER DNA BINDING PROTEIN/TRANSFERASE 19-FEB-03 1NZP TITLE SOLUTION STRUCTURE OF THE LYASE DOMAIN OF HUMAN DNA POLYMERASE LAMBDA COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE LAMBDA; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: POLYMERASE LAMBDA LYASE DOMAIN(RESIDUES 242 - 327); COMPND 5 SYNONYM: POL LAMBDA, DNA POLYMERASE LAMBDA, DNA POLYMERASE BETA-2, COMPND 6 POL BETA2; COMPND 7 EC: 2.7.7.7; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: POLL; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BLR (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET30A(+) KEYWDS DNA POLYMERASE LAMBDA, POL LAMBDA, LYASE DOMAIN, 8 KDA DOMAIN, POL KEYWDS 2 BETA-LIKE, DNA BINDING PROTEIN-TRANSFERASE COMPLEX EXPDTA SOLUTION NMR NUMMDL 8 MDLTYP MINIMIZED AVERAGE AUTHOR E.F.DEROSE,T.W.KIRBY,G.A.MUELLER,K.BEBENEK,M.GARCIA-DIAZ,L.BLANCO, AUTHOR 2 T.A.KUNKEL,R.E.LONDON REVDAT 3 23-FEB-22 1NZP 1 REMARK SEQADV REVDAT 2 24-FEB-09 1NZP 1 VERSN REVDAT 1 05-AUG-03 1NZP 0 JRNL AUTH E.F.DEROSE,T.W.KIRBY,G.A.MUELLER,K.BEBENEK,M.GARCIA-DIAZ, JRNL AUTH 2 L.BLANCO,T.A.KUNKEL,R.E.LONDON JRNL TITL SOLUTION STRUCTURE OF THE LYASE DOMAIN OF HUMAN DNA JRNL TITL 2 POLYMERASE LAMBDA JRNL REF BIOCHEMISTRY V. 42 9564 2003 JRNL REFN ISSN 0006-2960 JRNL PMID 12911298 JRNL DOI 10.1021/BI034298S REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : VNMR 6.1C, ARIA 1.1 REMARK 3 AUTHORS : VARIAN, INC. (VNMR), M. NILGES (ARIA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 THE STRUCTURE WAS COMPUTED USING DEFAULT ARIA PARAMETERS. REMARK 3 281 MANUALLY ASSIGNED NOE DISTANCE RESTRAINTS WERE USED REMARK 3 IN ADDITION TO THE NOE RESTRAINTS AUTOMATICALLY ASSIGNED REMARK 3 BY ARIA. ARIA ASSIGNED 790 UNAMBIGUOUS AND 191 AMBIGUOUS REMARK 3 NOE RESTRAINTS. REMARK 4 REMARK 4 1NZP COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-FEB-03. REMARK 100 THE DEPOSITION ID IS D_1000018394. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7 REMARK 210 IONIC STRENGTH : 5MM TRIS, 100MM NACL, 5MM NAN3 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 2MM POL LAMBDA 8 KDA DOMAIN U REMARK 210 -15N,13C; 5MM TRIS-D11; 100MM REMARK 210 NACL; 1MM DTT; 5MM NAN3 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C-SEPARATED_NOESY; 3D_15N REMARK 210 -SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 2.1, NMRVIEW 5.0.4, CNS REMARK 210 1.0, ARIA 1.1 REMARK 210 METHOD USED : SIMULATED ANNEALING TORSION REMARK 210 ANGLE DYNAMICS FOLLOW BY REMARK 210 CARTESIAN DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 20 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 8 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: CHEMICAL SHIFT ASSIGMENTS WERE MADE FROM 3D HNCACB, REMARK 210 CBCA(CO)NH, HNCO, H(CCO)NH, AND (H)C(CO)NH EXPERIMENTS. REMARK 210 AROMATIC RESONANCES WERE ASSIGNED USING 2D (HB)CB(CGCD)HD REMARK 210 AND (HB)CB(CGCDCE)HE EXPERIMENTS. 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-8 REMARK 465 RES C SSSEQI REMARK 465 MET A 241 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 1 PRO A 244 -119.91 -78.91 REMARK 500 1 SER A 245 89.10 58.61 REMARK 500 1 LYS A 248 -162.26 -129.58 REMARK 500 1 ASN A 251 174.28 -58.70 REMARK 500 1 ASN A 253 -81.89 -99.70 REMARK 500 1 LEU A 254 -2.32 58.56 REMARK 500 1 PRO A 292 -173.87 -66.17 REMARK 500 1 THR A 294 -40.26 -138.75 REMARK 500 1 HIS A 321 -74.62 -146.90 REMARK 500 1 LEU A 322 -72.07 -129.37 REMARK 500 2 SER A 246 10.82 -168.64 REMARK 500 2 ASN A 253 49.32 -157.92 REMARK 500 2 ASP A 272 87.18 -66.36 REMARK 500 2 THR A 294 -32.75 -136.39 REMARK 500 2 GLU A 318 -34.14 71.16 REMARK 500 2 SER A 319 109.25 58.24 REMARK 500 2 HIS A 321 11.83 -144.98 REMARK 500 3 GLN A 243 84.76 56.20 REMARK 500 3 PRO A 244 47.36 -80.00 REMARK 500 3 LYS A 248 77.42 55.02 REMARK 500 3 HIS A 255 2.35 -65.99 REMARK 500 3 THR A 294 -40.65 -131.13 REMARK 500 3 GLU A 318 -106.15 -141.45 REMARK 500 3 SER A 319 94.34 47.31 REMARK 500 3 LEU A 322 84.22 -59.00 REMARK 500 3 ARG A 323 101.52 -55.79 REMARK 500 4 PRO A 244 -175.95 -66.24 REMARK 500 4 SER A 245 -31.48 -168.43 REMARK 500 4 SER A 246 -86.74 60.55 REMARK 500 4 GLN A 247 -162.79 58.80 REMARK 500 4 HIS A 252 -56.16 -131.36 REMARK 500 4 ASN A 253 -68.03 -138.22 REMARK 500 4 LEU A 254 37.25 39.36 REMARK 500 4 ASP A 272 84.38 -157.22 REMARK 500 4 GLU A 318 -82.90 -42.09 REMARK 500 5 GLN A 247 -83.80 62.91 REMARK 500 5 SER A 288 21.11 -153.35 REMARK 500 5 HIS A 290 -66.55 -107.63 REMARK 500 5 PRO A 292 155.25 -48.87 REMARK 500 5 THR A 294 -43.55 -133.13 REMARK 500 5 GLU A 318 -90.09 -68.92 REMARK 500 5 SER A 319 -96.62 50.32 REMARK 500 6 SER A 246 -81.89 -70.95 REMARK 500 6 GLN A 247 -12.86 -167.75 REMARK 500 6 PRO A 292 -173.77 -68.96 REMARK 500 6 GLU A 318 7.57 59.65 REMARK 500 7 SER A 246 -77.12 -130.11 REMARK 500 7 LYS A 248 71.19 -103.60 REMARK 500 7 THR A 250 106.61 -47.05 REMARK 500 7 ASN A 253 19.72 -150.04 REMARK 500 REMARK 500 THIS ENTRY HAS 68 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL DBREF 1NZP A 242 327 UNP Q9UGP5 DPOL_HUMAN 242 327 SEQADV 1NZP MET A 241 UNP Q9UGP5 CLONING ARTIFACT SEQRES 1 A 87 MET ALA GLN PRO SER SER GLN LYS ALA THR ASN HIS ASN SEQRES 2 A 87 LEU HIS ILE THR GLU LYS LEU GLU VAL LEU ALA LYS ALA SEQRES 3 A 87 TYR SER VAL GLN GLY ASP LYS TRP ARG ALA LEU GLY TYR SEQRES 4 A 87 ALA LYS ALA ILE ASN ALA LEU LYS SER PHE HIS LYS PRO SEQRES 5 A 87 VAL THR SER TYR GLN GLU ALA CYS SER ILE PRO GLY ILE SEQRES 6 A 87 GLY LYS ARG MET ALA GLU LYS ILE ILE GLU ILE LEU GLU SEQRES 7 A 87 SER GLY HIS LEU ARG LYS LEU ASP HIS HELIX 1 1 LEU A 254 GLY A 271 1 18 HELIX 2 2 ASP A 272 LYS A 287 1 16 HELIX 3 3 SER A 295 SER A 301 1 7 HELIX 4 4 GLY A 306 GLU A 318 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