HEADER TRANSFERASE 13-JUN-06 2HAJ TITLE SOLUTION STRUCTURE OF THE HELICASE-BINDING DOMAIN OF ESCHERICHIA COLI TITLE 2 PRIMASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA PRIMASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: HELICASE-BINDING DOMAIN, RESIDUES 447-581; COMPND 5 EC: 2.7.7.-; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: DNAG; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMIDE; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PKL1176 KEYWDS DNA POLYMERASE, HELICASE, PRIMASE, HELIX, TRANSFERASE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR X.C.SU,K.V.LOSCHA,N.E.DIXON,G.OTTING REVDAT 6 15-MAY-24 2HAJ 1 REMARK REVDAT 5 14-JUN-23 2HAJ 1 REMARK REVDAT 4 26-FEB-20 2HAJ 1 REMARK REVDAT 3 24-FEB-09 2HAJ 1 VERSN REVDAT 2 07-NOV-06 2HAJ 1 JRNL REVDAT 1 17-OCT-06 2HAJ 0 JRNL AUTH X.C.SU,P.M.SCHAEFFER,K.V.LOSCHA,P.H.P.GAN,N.E.DIXON,G.OTTING JRNL TITL MONOMERIC SOLUTION STRUCTURE OF THE HELICASE-BINDING DOMAIN JRNL TITL 2 OF ESCHERICHIA COLI DNAG PRIMASE JRNL REF FEBS J. V. 273 4997 2006 JRNL REFN ISSN 1742-464X JRNL PMID 17010164 JRNL DOI 10.1111/J.1742-4658.2006.05495.X REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA 2.0, CYANA 2.0 REMARK 3 AUTHORS : GUNTERT, P. (CYANA), GUNTERT, P. (CYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2HAJ COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 14-JUN-06. REMARK 100 THE DEPOSITION ID IS D_1000038134. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.10 REMARK 210 IONIC STRENGTH : 100MM NACL REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.3MM DNAG-C U-15N, 13C; 10MM REMARK 210 PHOSPHATE BUFFER(PH 6.10); 100MM REMARK 210 NACL; 90% H2O, 10% D2O; 0.3MM REMARK 210 DNAG-C; 10MM PHOSPHATE BUFFER(PH REMARK 210 6.10); 100MM NACL; 90% H2O, 10% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C-SEPARATED_NOESY; 3D_15N REMARK 210 -SEPARATED_NOESY; (H)CCH-TOCSY; REMARK 210 CC(CO)NH; 2D NOESY; 2D TOCSY; REMARK 210 DQF-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN 1.3, CARA 1.2, SPARKY REMARK 210 1.5 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 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 ALA A 434 REMARK 465 ALA A 435 REMARK 465 GLU A 436 REMARK 465 SER A 437 REMARK 465 GLY A 438 REMARK 465 VAL A 439 REMARK 465 SER A 440 REMARK 465 ARG A 441 REMARK 465 PRO A 442 REMARK 465 VAL A 443 REMARK 465 PRO A 444 REMARK 465 GLN A 445 REMARK 465 LEU A 446 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE 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 1 ARG A 508 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 1 LEU A 519 CB - CG - CD1 ANGL. DEV. = 10.5 DEGREES REMARK 500 3 VAL A 468 CG1 - CB - CG2 ANGL. DEV. = -10.7 DEGREES REMARK 500 6 ARG A 486 NE - CZ - NH2 ANGL. DEV. = -3.9 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 THR A 450 175.09 57.49 REMARK 500 1 LEU A 474 -71.83 -115.06 REMARK 500 1 ASP A 475 166.90 59.97 REMARK 500 1 PRO A 480 78.11 -68.46 REMARK 500 1 ILE A 525 -63.14 -150.17 REMARK 500 1 ALA A 526 21.43 47.62 REMARK 500 1 LYS A 528 -30.11 -135.11 REMARK 500 1 THR A 560 -88.74 -139.73 REMARK 500 2 MET A 451 -41.50 69.91 REMARK 500 2 LEU A 471 68.58 66.21 REMARK 500 2 GLU A 472 -70.53 -63.98 REMARK 500 2 LEU A 474 -89.15 -90.26 REMARK 500 2 ASP A 475 158.44 64.19 REMARK 500 2 GLN A 495 104.24 -57.91 REMARK 500 2 THR A 560 -68.88 -96.55 REMARK 500 2 LEU A 563 157.65 -44.90 REMARK 500 2 LYS A 580 167.12 62.75 REMARK 500 3 MET A 451 11.92 -67.90 REMARK 500 3 PRO A 470 4.37 -69.34 REMARK 500 3 LEU A 471 55.62 71.76 REMARK 500 3 LEU A 474 -75.99 -88.38 REMARK 500 3 ASP A 475 159.03 63.73 REMARK 500 3 PRO A 480 77.84 -68.77 REMARK 500 3 SER A 494 -61.72 -93.41 REMARK 500 3 GLN A 495 91.88 -48.91 REMARK 500 3 ALA A 526 -94.79 -162.70 REMARK 500 3 ARG A 557 2.24 -67.96 REMARK 500 3 THR A 560 -67.40 -124.44 REMARK 500 3 HIS A 561 -68.06 -95.59 REMARK 500 3 SER A 564 172.93 -58.86 REMARK 500 3 ALA A 579 -88.12 -157.40 REMARK 500 3 LYS A 580 148.43 -172.70 REMARK 500 4 ARG A 448 69.79 64.53 REMARK 500 4 THR A 450 28.92 -150.07 REMARK 500 4 MET A 451 -38.83 75.68 REMARK 500 4 LEU A 471 65.82 71.09 REMARK 500 4 GLU A 472 -72.98 -73.23 REMARK 500 4 LEU A 474 -85.52 -87.14 REMARK 500 4 ASP A 475 152.13 62.47 REMARK 500 4 ILE A 525 -78.58 -122.19 REMARK 500 4 GLU A 558 -61.78 -104.25 REMARK 500 4 HIS A 561 -64.51 -93.42 REMARK 500 4 LYS A 580 -174.61 71.72 REMARK 500 5 ARG A 448 176.70 70.46 REMARK 500 5 THR A 449 -77.71 -113.51 REMARK 500 5 MET A 451 3.12 52.62 REMARK 500 5 PRO A 470 12.87 -67.57 REMARK 500 5 LEU A 471 8.34 80.67 REMARK 500 5 LEU A 474 -86.29 -71.21 REMARK 500 5 ASP A 475 140.97 58.96 REMARK 500 REMARK 500 THIS ENTRY HAS 178 RAMACHANDRAN OUTLIERS. 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 1 ARG A 559 0.10 SIDE CHAIN REMARK 500 17 TYR A 507 0.07 SIDE CHAIN REMARK 500 18 ARG A 486 0.10 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 4 SER A 538 11.09 REMARK 500 11 ASN A 540 -11.27 REMARK 500 16 THR A 573 -10.76 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1T3W RELATED DB: PDB REMARK 900 THE CRYSTAL STRUCTURE OF THE SAME PROTEIN REMARK 900 RELATED ID: 6284 RELATED DB: BMRB DBREF 2HAJ A 434 581 UNP P0ABS5 PRIM_ECOLI 434 581 SEQRES 1 A 148 ALA ALA GLU SER GLY VAL SER ARG PRO VAL PRO GLN LEU SEQRES 2 A 148 LYS ARG THR THR MET ARG ILE LEU ILE GLY LEU LEU VAL SEQRES 3 A 148 GLN ASN PRO GLU LEU ALA THR LEU VAL PRO PRO LEU GLU SEQRES 4 A 148 ASN LEU ASP GLU ASN LYS LEU PRO GLY LEU GLY LEU PHE SEQRES 5 A 148 ARG GLU LEU VAL ASN THR CYS LEU SER GLN PRO GLY LEU SEQRES 6 A 148 THR THR GLY GLN LEU LEU GLU HIS TYR ARG GLY THR ASN SEQRES 7 A 148 ASN ALA ALA THR LEU GLU LYS LEU SER MET TRP ASP ASP SEQRES 8 A 148 ILE ALA ASP LYS ASN ILE ALA GLU GLN THR PHE THR ASP SEQRES 9 A 148 SER LEU ASN HIS MET PHE ASP SER LEU LEU GLU LEU ARG SEQRES 10 A 148 GLN GLU GLU LEU ILE ALA ARG GLU ARG THR HIS GLY LEU SEQRES 11 A 148 SER ASN GLU GLU ARG LEU GLU LEU TRP THR LEU ASN GLN SEQRES 12 A 148 GLU LEU ALA LYS LYS HELIX 1 1 THR A 449 ASN A 461 1 13 HELIX 2 2 GLU A 463 VAL A 468 1 6 HELIX 3 3 LEU A 474 LEU A 479 1 6 HELIX 4 4 GLY A 481 GLN A 495 1 15 HELIX 5 5 THR A 499 TYR A 507 1 9 HELIX 6 6 ASN A 512 MET A 521 1 10 HELIX 7 7 LYS A 528 ARG A 559 1 32 HELIX 8 8 SER A 564 ALA A 579 1 16 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 MODEL 1