10 20 30 40 50 60 70 80 2HAJ - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER TRANSFERASE 13-JUN-06 2HAJ
TITLE SOLUTION STRUCTURE OF THE HELICASE-BINDING DOMAIN OF TITLE 2 ESCHERICHIA COLI 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 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, JRNL AUTH 2 N.E.DIXON,G.OTTING JRNL TITL MONOMERIC SOLUTION STRUCTURE OF THE JRNL TITL 2 HELICASE-BINDING DOMAIN OF ESCHERICHIA COLI DNAG JRNL TITL 3 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 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA 2.0 REMARK 3 AUTHORS : GUNTERT, P. 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 RCSB ID CODE IS RCSB038134.
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); REMARK 210 100MM NACL; 90% H2O, 10% D2O; REMARK 210 0.3MM DNAG-C; 10MM PHOSPHATE REMARK 210 BUFFER(PH 6.10); 100MM NACL; REMARK 210 90% H2O, 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C-SEPARATED_NOESY, 3D_ REMARK 210 15N-SEPARATED_NOESY, (H)CCH- REMARK 210 TOCSY, CC(CO)NH, 2D NOESY, 2D REMARK 210 TOCSY, 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 : CYANA 2.0, TOPSPIN 1.3, CARA REMARK 210 1.2, SPARKY 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 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: 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 5 PRO A 480 90.15 -68.76 REMARK 500 5 ASP A 523 -0.78 -57.55 REMARK 500 5 THR A 560 -85.89 -148.92 REMARK 500 5 LYS A 580 -71.95 49.43 REMARK 500 6 PRO A 470 0.51 -69.83 REMARK 500 6 LEU A 471 39.92 76.04 REMARK 500 6 LEU A 474 -74.29 -112.40 REMARK 500 6 ASP A 475 169.24 60.06 REMARK 500 6 ILE A 525 -70.67 -108.38 REMARK 500 6 LYS A 580 92.84 14.98 REMARK 500 7 LEU A 474 -77.14 -82.49 REMARK 500 7 ASP A 475 150.87 65.83 REMARK 500 7 PRO A 480 87.04 -67.90 REMARK 500 7 THR A 560 -87.98 -138.65 REMARK 500 7 LEU A 563 160.63 -48.53 REMARK 500 7 ALA A 579 76.62 35.43 REMARK 500 7 LYS A 580 93.83 -53.86 REMARK 500 8 THR A 449 -144.99 46.65 REMARK 500 8 MET A 451 40.85 -75.86 REMARK 500 8 PRO A 470 8.95 -65.93 REMARK 500 8 LEU A 471 -0.13 90.49 REMARK 500 8 ASP A 475 118.80 57.88 REMARK 500 8 PRO A 480 85.23 -67.16 REMARK 500 8 MET A 521 33.26 -87.45 REMARK 500 8 ILE A 525 -60.36 -137.87 REMARK 500 8 ALA A 526 0.86 53.85 REMARK 500 8 LYS A 528 -25.84 -142.98 REMARK 500 8 THR A 560 -81.78 -143.28 REMARK 500 9 ARG A 448 174.02 69.89 REMARK 500 9 LEU A 471 58.76 72.95 REMARK 500 9 LEU A 474 -94.90 -106.41 REMARK 500 9 ASP A 475 142.99 78.92 REMARK 500 9 PRO A 480 1.95 -69.28 REMARK 500 9 GLN A 495 93.06 -46.24 REMARK 500 9 ILE A 525 -77.91 -113.31 REMARK 500 9 THR A 560 -105.33 -113.38 REMARK 500 9 LYS A 580 86.41 37.42 REMARK 500 10 ARG A 448 -79.16 -55.96 REMARK 500 10 LEU A 471 47.81 71.18 REMARK 500 10 LEU A 474 -78.53 -109.10 REMARK 500 10 ASP A 475 162.73 62.61 REMARK 500 10 ILE A 525 -78.64 -57.61 REMARK 500 10 ALA A 526 -86.70 -171.28 REMARK 500 10 THR A 560 -89.31 -138.63 REMARK 500 10 LEU A 563 158.27 -48.45 REMARK 500 11 ARG A 448 177.65 179.52 REMARK 500 11 THR A 449 112.68 64.02 REMARK 500 11 PRO A 470 3.87 -68.49 REMARK 500 11 LEU A 471 63.47 68.54 REMARK 500 11 LEU A 474 -91.15 -84.16 REMARK 500 11 ASP A 475 150.36 65.02 REMARK 500 11 PRO A 480 76.51 -68.96 REMARK 500 11 ILE A 525 -70.84 -110.27 REMARK 500 11 HIS A 561 -74.18 -115.06 REMARK 500 11 LYS A 580 -59.86 -147.45 REMARK 500 12 THR A 450 -91.86 -120.45 REMARK 500 12 MET A 451 -40.39 -164.53 REMARK 500 12 LEU A 474 -58.21 -124.13 REMARK 500 12 ASP A 475 157.25 64.59 REMARK 500 12 PRO A 480 87.95 -66.53 REMARK 500 12 ILE A 525 -64.62 -125.76 REMARK 500 12 ALA A 526 3.08 50.38 REMARK 500 12 THR A 560 -79.98 -148.18 REMARK 500 13 THR A 449 123.39 65.62 REMARK 500 13 LEU A 471 70.49 68.63 REMARK 500 13 GLU A 472 -62.51 -100.68 REMARK 500 13 LEU A 474 -61.97 -90.88 REMARK 500 13 ASP A 475 152.81 60.77 REMARK 500 13 LEU A 563 -174.50 -55.83 REMARK 500 13 LYS A 580 73.51 -154.34 REMARK 500 14 ARG A 448 -88.65 53.59 REMARK 500 14 THR A 450 58.06 -161.21 REMARK 500 14 ARG A 452 -46.28 -132.76 REMARK 500 14 LEU A 471 60.59 61.79 REMARK 500 14 GLU A 472 -68.88 -90.55 REMARK 500 14 LEU A 474 -81.72 -100.99 REMARK 500 14 ASP A 475 153.28 62.95 REMARK 500 14 ILE A 525 -71.37 -135.85 REMARK 500 14 ALA A 526 -89.87 -170.67 REMARK 500 14 THR A 560 -81.44 -131.89 REMARK 500 14 HIS A 561 -77.18 -56.12 REMARK 500 14 ALA A 579 56.00 33.93 REMARK 500 14 LYS A 580 75.32 62.88 REMARK 500 15 ARG A 448 59.05 91.66 REMARK 500 15 THR A 449 -161.75 -129.19 REMARK 500 15 LEU A 474 -56.45 -122.88 REMARK 500 15 GLU A 476 -11.66 53.67 REMARK 500 16 THR A 450 -85.95 -146.27 REMARK 500 16 MET A 451 -44.05 -165.74 REMARK 500 16 LEU A 474 -77.56 -97.64 REMARK 500 16 ASP A 475 141.42 64.41 REMARK 500 16 ILE A 525 -66.88 -123.53 REMARK 500 16 LEU A 563 -159.05 41.17 REMARK 500 16 ALA A 579 50.07 31.23 REMARK 500 16 LYS A 580 78.37 63.44 REMARK 500 17 ARG A 448 -68.51 -99.17 REMARK 500 17 THR A 450 39.40 -152.80 REMARK 500 17 MET A 451 -38.89 79.60 REMARK 500 17 LEU A 471 70.35 69.09 REMARK 500 17 ASP A 475 25.45 46.39 REMARK 500 17 GLU A 476 26.39 40.90 REMARK 500 17 THR A 560 -88.51 -101.11 REMARK 500 17 LEU A 563 159.34 -41.21 REMARK 500 17 ALA A 579 -53.05 67.25 REMARK 500 18 ARG A 448 166.46 105.91 REMARK 500 18 THR A 449 136.55 53.01 REMARK 500 18 PRO A 470 13.07 -67.05 REMARK 500 18 LEU A 471 46.01 72.08 REMARK 500 18 GLU A 472 -83.32 -66.39 REMARK 500 18 LEU A 474 -76.62 -74.80 REMARK 500 18 ASP A 475 131.71 62.25 REMARK 500 18 PRO A 480 2.74 -68.96 REMARK 500 18 ILE A 525 -63.28 -127.12 REMARK 500 18 ALA A 526 25.12 46.27 REMARK 500 18 THR A 560 -88.52 -95.98 REMARK 500 19 ARG A 448 76.15 49.18 REMARK 500 19 MET A 451 29.76 49.42 REMARK 500 19 LEU A 471 43.07 72.46 REMARK 500 19 LEU A 474 -101.68 -100.85 REMARK 500 19 ASP A 475 147.15 70.97 REMARK 500 19 ALA A 526 52.02 37.94 REMARK 500 19 THR A 560 -82.40 -99.60 REMARK 500 20 ARG A 448 -67.70 -150.92 REMARK 500 20 ARG A 452 -51.29 -146.01 REMARK 500 20 LEU A 474 -71.41 -128.66 REMARK 500 20 ASP A 475 162.61 60.71 REMARK 500 20 GLN A 495 98.40 -57.20 REMARK 500 20 ALA A 579 81.14 50.83 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, 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