HEADER TRANSFERASE 04-OCT-12 2LZN TITLE SOLUTION STRUCTURE OF S. AUREUS PRIMASE C-TERMINAL DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA PRIMASE; COMPND 3 CHAIN: A; COMPND 4 EC: 2.7.7.-; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS; SOURCE 3 ORGANISM_TAXID: 158878; SOURCE 4 STRAIN: MU50 / ATCC 700699; SOURCE 5 GENE: DNAG, SAV1562; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DNAG, PRIMASE, HELICASE, DNAB, TRANSFERASE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR M.D.SHORTRIDGE,M.A.GRIEP,R.POWERS REVDAT 1 09-OCT-13 2LZN 0 JRNL AUTH M.D.SHORTRIDGE,M.A.GRIEP,R.POWERS JRNL TITL SOLUTION STRUCTURE OF S. AUREUS PRIMASE C-TERMINAL DOMAIN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.D.SHORTRIDGE,M.A.GRIEP,R.POWERS REMARK 1 TITL 1H, 13C, AND 15N NMR ASSIGNMENTS FOR THE HELICASE REMARK 1 TITL 2 INTERACTION DOMAIN OF STAPHYLOCOCCUS AUREUS DNAG PRIMASE. REMARK 1 REF BIOMOL.NMR ASSIGN. V. 6 35 2012 REMARK 1 REFN ISSN 1874-2718 REMARK 1 PMID 21644056 REMARK 1 DOI 10.1007/S12104-011-9320-7 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XPLOR-NIH REMARK 3 AUTHORS : DELAGLIO, GRZESIEK, VUISTER, ZHU, PFEIFER AND BAX REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2LZN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-OCT-12. REMARK 100 THE RCSB ID CODE IS RCSB103024. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.6 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1.4 MM [U-100% 13C; U-100% 15N] REMARK 210 PRIMASE CTD, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 2D 1H-13C HSQC ALIPHATIC; 2D 1H- REMARK 210 13C HSQC AROMATIC; 3D CBCA(CO)NH; REMARK 210 3D HNCO; 3D HNCA; 3D HNCACB; 3D REMARK 210 HCCH-COSY; 3D HN(CO)CA; 3D 1H-15N REMARK 210 NOESY; 3D 1H-13C NOESY ALIPHATIC; REMARK 210 3D 1H-13C NOESY AROMATIC; 3D HNHA REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE REMARK 210 METHOD USED : DGSA-DISTANCE GEOMETRY SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 2000 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST ENERGY 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 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 HZ2 LYS A 505 OE1 GLU A 509 1.59 REMARK 500 HZ2 LYS A 478 OE1 GLU A 550 1.59 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 17 TYR A 490 CD1 TYR A 490 CE1 -0.097 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 ASN A 533 C - N - CA ANGL. DEV. = 17.3 DEGREES REMARK 500 7 ASN A 533 C - N - CA ANGL. DEV. = 15.6 DEGREES REMARK 500 11 ASN A 533 C - N - CA ANGL. DEV. = 15.4 DEGREES REMARK 500 17 ASN A 533 C - N - CA ANGL. DEV. = 16.8 DEGREES REMARK 500 19 ASN A 533 C - N - CA ANGL. DEV. = 17.1 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 ASN A 465 56.60 -114.15 REMARK 500 1 LEU A 466 98.08 -66.60 REMARK 500 1 ASP A 497 -72.04 -69.80 REMARK 500 1 GLU A 517 -57.76 -134.13 REMARK 500 1 SER A 532 -144.07 -75.51 REMARK 500 1 ASN A 533 30.94 -26.64 REMARK 500 1 GLU A 534 -5.91 -30.07 REMARK 500 1 GLU A 555 -92.74 -78.98 REMARK 500 1 ARG A 583 1.86 -53.67 REMARK 500 1 VAL A 587 23.22 -46.62 REMARK 500 1 GLU A 588 -2.63 -43.11 REMARK 500 2 LEU A 466 161.30 -49.23 REMARK 500 2 MET A 481 3.28 -67.13 REMARK 500 2 ASP A 519 -154.84 -76.41 REMARK 500 2 ASN A 533 -73.76 -69.12 REMARK 500 2 PRO A 551 129.17 -36.79 REMARK 500 2 GLN A 568 105.67 50.99 REMARK 500 2 ARG A 583 -2.90 -51.42 REMARK 500 2 VAL A 587 -19.39 -48.50 REMARK 500 3 LEU A 466 80.84 -67.36 REMARK 500 3 HIS A 479 161.31 46.29 REMARK 500 3 LEU A 480 -154.66 -143.21 REMARK 500 3 ASP A 483 31.29 -76.60 REMARK 500 3 ASP A 495 45.64 -86.63 REMARK 500 3 ASN A 518 -151.27 -59.61 REMARK 500 3 ASP A 519 -152.75 -31.54 REMARK 500 3 ASN A 533 -84.00 -68.11 REMARK 500 3 PRO A 551 38.74 -84.63 REMARK 500 3 GLU A 569 133.19 79.39 REMARK 500 3 VAL A 587 -4.67 -54.63 REMARK 500 4 HIS A 479 89.70 -170.15 REMARK 500 4 MET A 481 -72.68 -83.60 REMARK 500 4 ASN A 518 -151.01 -121.16 REMARK 500 4 ASP A 519 -160.62 -76.84 REMARK 500 4 ASN A 533 -72.23 -57.84 REMARK 500 4 LEU A 547 -82.54 -92.35 REMARK 500 4 ASP A 549 36.25 -68.23 REMARK 500 4 GLU A 550 106.11 -54.97 REMARK 500 4 TYR A 552 -54.14 -131.26 REMARK 500 4 GLU A 569 152.88 72.02 REMARK 500 4 THR A 570 -60.21 71.29 REMARK 500 4 ARG A 583 -2.91 -51.12 REMARK 500 4 VAL A 587 -5.15 -56.92 REMARK 500 5 ASN A 465 47.82 -91.64 REMARK 500 5 LEU A 466 95.12 -67.23 REMARK 500 5 HIS A 479 -97.15 40.05 REMARK 500 5 ASP A 483 41.28 -70.55 REMARK 500 5 LYS A 496 -90.89 -89.23 REMARK 500 5 ASP A 497 -85.22 -106.25 REMARK 500 5 ASN A 498 -50.67 -127.79 REMARK 500 REMARK 500 THIS ENTRY HAS 273 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ASN A 518 ASP A 519 3 -138.33 REMARK 500 ASP A 519 GLN A 520 3 -145.04 REMARK 500 ASN A 498 PHE A 499 5 -149.65 REMARK 500 ASN A 518 ASP A 519 15 -136.82 REMARK 500 ASP A 519 GLN A 520 15 -146.46 REMARK 500 ILE A 584 GLY A 585 16 -144.57 REMARK 500 ASP A 586 VAL A 587 16 -139.68 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 3 ARG A 579 0.08 SIDE CHAIN REMARK 500 5 ARG A 579 0.09 SIDE CHAIN REMARK 500 7 ARG A 474 0.08 SIDE CHAIN REMARK 500 8 ARG A 482 0.07 SIDE CHAIN REMARK 500 11 ARG A 536 0.15 SIDE CHAIN REMARK 500 12 ARG A 474 0.08 SIDE CHAIN REMARK 500 17 ARG A 579 0.09 SIDE CHAIN REMARK 500 18 ARG A 536 0.09 SIDE CHAIN REMARK 500 18 ARG A 583 0.08 SIDE CHAIN REMARK 500 19 ARG A 536 0.17 SIDE CHAIN REMARK 500 19 ARG A 579 0.09 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 11 ASN A 533 12.04 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 1 LYS A 591 24.1 L L OUTSIDE RANGE REMARK 500 2 VAL A 530 24.2 L L OUTSIDE RANGE REMARK 500 3 ASP A 519 23.2 L L OUTSIDE RANGE REMARK 500 4 HIS A 576 21.5 L L OUTSIDE RANGE REMARK 500 5 GLU A 470 23.4 L L OUTSIDE RANGE REMARK 500 5 PHE A 499 22.0 L L OUTSIDE RANGE REMARK 500 5 GLN A 520 24.2 L L OUTSIDE RANGE REMARK 500 6 GLN A 595 23.9 L L OUTSIDE RANGE REMARK 500 9 VAL A 530 24.9 L L OUTSIDE RANGE REMARK 500 9 ARG A 583 23.2 L L OUTSIDE RANGE REMARK 500 10 VAL A 587 24.0 L L OUTSIDE RANGE REMARK 500 11 ASN A 533 18.3 L L OUTSIDE RANGE REMARK 500 11 GLU A 588 23.8 L L OUTSIDE RANGE REMARK 500 13 ASP A 483 23.6 L L OUTSIDE RANGE REMARK 500 13 VAL A 587 22.5 L L OUTSIDE RANGE REMARK 500 13 GLU A 588 24.2 L L OUTSIDE RANGE REMARK 500 15 GLN A 520 24.1 L L OUTSIDE RANGE REMARK 500 17 MET A 481 23.8 L L OUTSIDE RANGE REMARK 500 20 ASN A 533 22.8 L L OUTSIDE RANGE REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 17512 RELATED DB: BMRB DBREF 2LZN A 463 605 UNP P63964 PRIM_STAAM 463 605 SEQRES 1 A 143 PHE ASP ASN LEU SER ARG GLN GLU LYS ALA GLU ARG ALA SEQRES 2 A 143 PHE LEU LYS HIS LEU MET ARG ASP LYS ASP THR PHE LEU SEQRES 3 A 143 ASN TYR TYR GLU SER VAL ASP LYS ASP ASN PHE THR ASN SEQRES 4 A 143 GLN HIS PHE LYS TYR VAL PHE GLU VAL LEU HIS ASP PHE SEQRES 5 A 143 TYR ALA GLU ASN ASP GLN TYR ASN ILE SER ASP ALA VAL SEQRES 6 A 143 GLN TYR VAL ASN SER ASN GLU LEU ARG GLU THR LEU ILE SEQRES 7 A 143 SER LEU GLU GLN TYR ASN LEU ASN ASP GLU PRO TYR GLU SEQRES 8 A 143 ASN GLU ILE ASP ASP TYR VAL ASN VAL ILE ASN GLU LYS SEQRES 9 A 143 GLY GLN GLU THR ILE GLU SER LEU ASN HIS LYS LEU ARG SEQRES 10 A 143 GLU ALA THR ARG ILE GLY ASP VAL GLU LEU GLN LYS TYR SEQRES 11 A 143 TYR LEU GLN GLN ILE VAL ALA LYS ASN LYS GLU ARG MET HELIX 1 1 SER A 467 LEU A 477 1 11 HELIX 2 2 ASP A 483 VAL A 494 1 12 HELIX 3 3 ASN A 501 ALA A 516 1 16 HELIX 4 4 ASN A 522 TYR A 529 1 8 HELIX 5 5 GLU A 534 TYR A 545 1 12 HELIX 6 6 PRO A 551 ASN A 554 5 4 HELIX 7 7 GLU A 555 GLU A 565 1 11 HELIX 8 8 GLU A 572 ARG A 583 1 12 HELIX 9 9 LEU A 589 GLU A 603 1 15 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