PDB Short entry for 2KEB HEADER DNA BINDING PROTEIN 28-JAN-09 2KEB TITLE NMR SOLUTION STRUCTURE OF THE N-TERMINAL DOMAIN OF THE DNA POLYMERASE TITLE 2 ALPHA P68 SUBUNIT COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE SUBUNIT ALPHA B; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DNA POLYMERASE ALPHA 70 KDA SUBUNIT; COMPND 5 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: POLA2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PBG100 KEYWDS DNA POLYMERASE ALPHA, DNA REPLICATION, NUCLEUS, PHOSPHOPROTEIN, DNA KEYWDS 2 BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR H.HUANG,B.E.WEINER,H.ZHANG,B.E.FULLER,Y.GAO,B.M.WILE,W.J.CHAZIN, AUTHOR 2 E.FANNING REVDAT 3 16-MAR-22 2KEB 1 REMARK SEQADV REVDAT 2 14-JUL-10 2KEB 1 JRNL REVDAT 1 02-FEB-10 2KEB 0 JRNL AUTH H.HUANG,B.E.WEINER,H.ZHANG,B.E.FULLER,Y.GAO,B.M.WILE,K.ZHAO, JRNL AUTH 2 D.R.ARNETT,W.J.CHAZIN,E.FANNING JRNL TITL STRUCTURE OF A DNA POLYMERASE ALPHA-PRIMASE DOMAIN THAT JRNL TITL 2 DOCKS ON THE SV40 HELICASE AND ACTIVATES THE VIRAL JRNL TITL 3 PRIMOSOME. JRNL REF J.BIOL.CHEM. V. 285 17112 2010 JRNL REFN ISSN 0021-9258 JRNL PMID 20234039 JRNL DOI 10.1074/JBC.M110.116830 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA 2.1, AMBER 9 REMARK 3 AUTHORS : GUNTERT, P. ET AL. (CYANA), CASE, D. ET AL. REMARK 3 (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2KEB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-FEB-09. REMARK 100 THE DEPOSITION ID IS D_1000101014. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 0.05 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.75 MM [U-100% 13C; U-100% 15N] REMARK 210 PROTEIN, 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 3D 1H-15N NOESY; REMARK 210 3D 1H-13C NOESY; 4D 1H-13C NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA 2.1 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS 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: 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 1-20 REMARK 465 RES C SSSEQI REMARK 465 MET A -22 REMARK 465 GLY A -21 REMARK 465 SER A -20 REMARK 465 SER A -19 REMARK 465 HIS A -18 REMARK 465 HIS A -17 REMARK 465 HIS A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 GLY A -12 REMARK 465 SER A -11 REMARK 465 SER A -10 REMARK 465 LEU A -9 REMARK 465 GLU A -8 REMARK 465 VAL A -7 REMARK 465 LEU A -6 REMARK 465 PHE A -5 REMARK 465 GLN A -4 REMARK 465 GLY A -3 REMARK 465 PRO A -2 REMARK 465 GLY A -1 REMARK 465 SER A 0 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 2 ARG A 78 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 6 ARG A 78 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 18 ARG A 78 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 SER A 4 96.19 78.15 REMARK 500 1 PHE A 69 -45.49 -148.77 REMARK 500 2 PHE A 69 -39.60 -153.36 REMARK 500 2 ARG A 73 138.35 89.72 REMARK 500 2 ALA A 77 -40.89 -153.25 REMARK 500 3 ALA A 3 54.28 -163.16 REMARK 500 3 PHE A 69 -44.45 -151.69 REMARK 500 3 ARG A 73 141.45 167.28 REMARK 500 4 ALA A 3 -73.76 62.71 REMARK 500 4 SER A 4 147.86 80.35 REMARK 500 4 HIS A 53 0.16 85.82 REMARK 500 4 LEU A 57 164.63 69.72 REMARK 500 4 PHE A 69 -43.03 -140.23 REMARK 500 4 ARG A 73 138.12 174.46 REMARK 500 4 ALA A 77 -41.72 69.99 REMARK 500 5 ALA A 3 -60.59 -169.90 REMARK 500 5 HIS A 53 20.59 83.09 REMARK 500 5 PHE A 69 -42.72 -144.98 REMARK 500 6 SER A 2 41.54 -84.71 REMARK 500 6 PHE A 69 -49.71 -152.04 REMARK 500 7 SER A 4 131.83 76.66 REMARK 500 7 PHE A 48 -65.99 -94.43 REMARK 500 7 PHE A 69 -48.42 -150.36 REMARK 500 8 ASP A 18 46.92 -83.50 REMARK 500 8 HIS A 53 32.11 71.89 REMARK 500 8 PHE A 69 -43.96 -151.32 REMARK 500 9 HIS A 53 47.50 72.96 REMARK 500 9 VAL A 55 84.61 62.71 REMARK 500 10 PHE A 69 -60.64 -154.87 REMARK 500 10 ARG A 73 132.98 173.31 REMARK 500 11 ASP A 18 43.51 -80.99 REMARK 500 11 PHE A 69 -50.00 -147.72 REMARK 500 12 PHE A 69 -50.77 -152.68 REMARK 500 12 ARG A 73 -39.06 -151.58 REMARK 500 12 LEU A 74 -45.67 67.84 REMARK 500 12 SER A 75 5.95 83.05 REMARK 500 13 SER A 4 124.51 79.20 REMARK 500 13 PHE A 69 -48.14 -149.11 REMARK 500 13 ALA A 77 48.30 -84.44 REMARK 500 14 SER A 4 146.65 82.59 REMARK 500 14 HIS A 53 -1.93 80.38 REMARK 500 14 PHE A 69 -46.39 -158.69 REMARK 500 14 ARG A 73 138.73 89.24 REMARK 500 15 SER A 4 121.79 82.76 REMARK 500 15 HIS A 53 -0.66 79.56 REMARK 500 15 PHE A 69 -44.27 -156.02 REMARK 500 15 ARG A 73 135.32 175.92 REMARK 500 16 ASN A 37 163.84 72.75 REMARK 500 16 HIS A 53 42.45 80.31 REMARK 500 16 PHE A 69 -59.76 -148.49 REMARK 500 REMARK 500 THIS ENTRY HAS 60 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL DBREF 2KEB A 1 78 UNP Q14181 DPOA2_HUMAN 1 78 SEQADV 2KEB MET A -22 UNP Q14181 EXPRESSION TAG SEQADV 2KEB GLY A -21 UNP Q14181 EXPRESSION TAG SEQADV 2KEB SER A -20 UNP Q14181 EXPRESSION TAG SEQADV 2KEB SER A -19 UNP Q14181 EXPRESSION TAG SEQADV 2KEB HIS A -18 UNP Q14181 EXPRESSION TAG SEQADV 2KEB HIS A -17 UNP Q14181 EXPRESSION TAG SEQADV 2KEB HIS A -16 UNP Q14181 EXPRESSION TAG SEQADV 2KEB HIS A -15 UNP Q14181 EXPRESSION TAG SEQADV 2KEB HIS A -14 UNP Q14181 EXPRESSION TAG SEQADV 2KEB HIS A -13 UNP Q14181 EXPRESSION TAG SEQADV 2KEB GLY A -12 UNP Q14181 EXPRESSION TAG SEQADV 2KEB SER A -11 UNP Q14181 EXPRESSION TAG SEQADV 2KEB SER A -10 UNP Q14181 EXPRESSION TAG SEQADV 2KEB LEU A -9 UNP Q14181 EXPRESSION TAG SEQADV 2KEB GLU A -8 UNP Q14181 EXPRESSION TAG SEQADV 2KEB VAL A -7 UNP Q14181 EXPRESSION TAG SEQADV 2KEB LEU A -6 UNP Q14181 EXPRESSION TAG SEQADV 2KEB PHE A -5 UNP Q14181 EXPRESSION TAG SEQADV 2KEB GLN A -4 UNP Q14181 EXPRESSION TAG SEQADV 2KEB GLY A -3 UNP Q14181 EXPRESSION TAG SEQADV 2KEB PRO A -2 UNP Q14181 EXPRESSION TAG SEQADV 2KEB GLY A -1 UNP Q14181 EXPRESSION TAG SEQADV 2KEB SER A 0 UNP Q14181 EXPRESSION TAG SEQRES 1 A 101 MET GLY SER SER HIS HIS HIS HIS HIS HIS GLY SER SER SEQRES 2 A 101 LEU GLU VAL LEU PHE GLN GLY PRO GLY SER MET SER ALA SEQRES 3 A 101 SER ALA GLN GLN LEU ALA GLU GLU LEU GLN ILE PHE GLY SEQRES 4 A 101 LEU ASP CYS GLU GLU ALA LEU ILE GLU LYS LEU VAL GLU SEQRES 5 A 101 LEU CYS VAL GLN TYR GLY GLN ASN GLU GLU GLY MET VAL SEQRES 6 A 101 GLY GLU LEU ILE ALA PHE CYS THR SER THR HIS LYS VAL SEQRES 7 A 101 GLY LEU THR SER GLU ILE LEU ASN SER PHE GLU HIS GLU SEQRES 8 A 101 PHE LEU SER LYS ARG LEU SER LYS ALA ARG HELIX 1 1 SER A 4 GLY A 16 1 13 HELIX 2 2 GLU A 20 GLY A 35 1 16 HELIX 3 3 ASN A 37 HIS A 53 1 17 HELIX 4 4 THR A 58 PHE A 69 1 12 HELIX 5 5 PHE A 69 LEU A 74 1 6 CISPEP 1 MET A 1 SER A 2 10 -0.85 CISPEP 2 SER A 2 ALA A 3 19 -3.00 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