HEADER TRANSFERASE 27-MAR-12 4EDK TITLE THE STRUCTURE OF THE S. AUREUS DNAG RNA POLYMERASE DOMAIN BOUND TO GTP TITLE 2 AND MANGANESE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA PRIMASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 111-436; COMPND 5 EC: 2.7.7.-; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS; SOURCE 3 ORGANISM_TAXID: 1280; SOURCE 4 GENE: DNAG; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) CODON+; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28B KEYWDS CATALYTIC DOMAIN, NUCLEOSIDE TRIPHOSPHATE, NUCLEOSIDE POLYPHOSPHATE, KEYWDS 2 PROTEIN-LIGAND COMPLEX, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR R.U.RYMER,F.A.SOLORIO,C.CHU,J.E.CORN,J.D.WANG,J.M.BERGER REVDAT 4 28-FEB-24 4EDK 1 REMARK SEQADV LINK REVDAT 3 10-JUL-13 4EDK 1 JRNL REVDAT 2 01-AUG-12 4EDK 1 TITLE REVDAT 1 25-JUL-12 4EDK 0 JRNL AUTH R.U.RYMER,F.A.SOLORIO,A.K.TEHRANCHI,C.CHU,J.E.CORN,J.L.KECK, JRNL AUTH 2 J.D.WANG,J.M.BERGER JRNL TITL BINDING MECHANISM OF METAL-NTP SUBSTRATES AND JRNL TITL 2 STRINGENT-RESPONSE ALARMONES TO BACTERIAL DNAG-TYPE JRNL TITL 3 PRIMASES. JRNL REF STRUCTURE V. 20 1478 2012 JRNL REFN ISSN 0969-2126 JRNL PMID 22795082 JRNL DOI 10.1016/J.STR.2012.05.017 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.7.3_928 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.94 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 34983 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.163 REMARK 3 R VALUE (WORKING SET) : 0.161 REMARK 3 FREE R VALUE : 0.200 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.030 REMARK 3 FREE R VALUE TEST SET COUNT : 1760 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 37.9423 - 4.7001 1.00 2684 143 0.1608 0.1749 REMARK 3 2 4.7001 - 3.7317 1.00 2607 118 0.1382 0.1713 REMARK 3 3 3.7317 - 3.2603 1.00 2571 140 0.1606 0.2107 REMARK 3 4 3.2603 - 2.9623 1.00 2552 130 0.1671 0.2018 REMARK 3 5 2.9623 - 2.7501 1.00 2530 145 0.1691 0.2018 REMARK 3 6 2.7501 - 2.5880 1.00 2550 136 0.1677 0.2294 REMARK 3 7 2.5880 - 2.4584 1.00 2560 127 0.1566 0.1953 REMARK 3 8 2.4584 - 2.3514 1.00 2537 143 0.1554 0.1847 REMARK 3 9 2.3514 - 2.2609 1.00 2511 144 0.1683 0.2068 REMARK 3 10 2.2609 - 2.1829 1.00 2551 125 0.1856 0.2524 REMARK 3 11 2.1829 - 2.1146 1.00 2541 142 0.1720 0.2505 REMARK 3 12 2.1146 - 2.0542 1.00 2469 136 0.1719 0.2258 REMARK 3 13 2.0542 - 2.0001 1.00 2560 131 0.1729 0.2129 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.20 REMARK 3 SHRINKAGE RADIUS : 0.98 REMARK 3 K_SOL : 0.32 REMARK 3 B_SOL : 39.62 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.660 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.25 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.03940 REMARK 3 B22 (A**2) : 1.03940 REMARK 3 B33 (A**2) : -2.07890 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.005 2702 REMARK 3 ANGLE : 0.932 3649 REMARK 3 CHIRALITY : 0.060 392 REMARK 3 PLANARITY : 0.004 470 REMARK 3 DIHEDRAL : 15.887 1014 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 108:233) REMARK 3 ORIGIN FOR THE GROUP (A): -41.7257 -54.0200 -3.7274 REMARK 3 T TENSOR REMARK 3 T11: 0.2658 T22: 0.1107 REMARK 3 T33: 0.0865 T12: -0.0751 REMARK 3 T13: -0.0199 T23: -0.0003 REMARK 3 L TENSOR REMARK 3 L11: 0.4678 L22: 1.5217 REMARK 3 L33: 2.6371 L12: 0.2320 REMARK 3 L13: -0.4981 L23: 0.0156 REMARK 3 S TENSOR REMARK 3 S11: 0.0063 S12: 0.0415 S13: -0.0047 REMARK 3 S21: -0.0451 S22: -0.0051 S23: 0.0118 REMARK 3 S31: 0.0670 S32: -0.2735 S33: 0.0103 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 234:343) REMARK 3 ORIGIN FOR THE GROUP (A): -28.9050 -35.7264 5.9179 REMARK 3 T TENSOR REMARK 3 T11: 0.2336 T22: 0.0777 REMARK 3 T33: 0.1747 T12: -0.0386 REMARK 3 T13: -0.0793 T23: -0.0049 REMARK 3 L TENSOR REMARK 3 L11: 1.9987 L22: 2.1000 REMARK 3 L33: 0.7027 L12: 1.3381 REMARK 3 L13: 0.0871 L23: 0.1000 REMARK 3 S TENSOR REMARK 3 S11: -0.0156 S12: -0.0948 S13: 0.0475 REMARK 3 S21: 0.1594 S22: -0.0238 S23: -0.1809 REMARK 3 S31: 0.0678 S32: -0.0296 S33: -0.0211 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 344:362) REMARK 3 ORIGIN FOR THE GROUP (A): -16.8152 -35.9779 -6.9620 REMARK 3 T TENSOR REMARK 3 T11: 0.3390 T22: 0.3106 REMARK 3 T33: 0.3738 T12: -0.0488 REMARK 3 T13: -0.0074 T23: -0.0848 REMARK 3 L TENSOR REMARK 3 L11: 0.2417 L22: 0.2579 REMARK 3 L33: 0.2971 L12: -0.1062 REMARK 3 L13: -0.1675 L23: -0.1220 REMARK 3 S TENSOR REMARK 3 S11: -0.0593 S12: 0.4512 S13: -0.0689 REMARK 3 S21: -0.3622 S22: 0.2379 S23: -0.1395 REMARK 3 S31: -0.1794 S32: 0.4792 S33: 0.0002 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 363:428) REMARK 3 ORIGIN FOR THE GROUP (A): -21.7437 -12.4160 8.1411 REMARK 3 T TENSOR REMARK 3 T11: 0.1933 T22: 0.1242 REMARK 3 T33: 0.3502 T12: -0.0313 REMARK 3 T13: -0.0751 T23: -0.0243 REMARK 3 L TENSOR REMARK 3 L11: 1.4037 L22: 1.3703 REMARK 3 L33: 1.2359 L12: 0.3690 REMARK 3 L13: -0.4795 L23: -0.5848 REMARK 3 S TENSOR REMARK 3 S11: -0.0055 S12: -0.0782 S13: 0.2824 REMARK 3 S21: 0.1750 S22: 0.0719 S23: -0.1983 REMARK 3 S31: -0.0892 S32: 0.0014 S33: -0.0219 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4EDK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-MAR-12. REMARK 100 THE DEPOSITION ID IS D_1000071482. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-NOV-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.3.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.115 REMARK 200 MONOCHROMATOR : DOUBLE FLAT CRYSTAL, SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.16 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35005 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 37.935 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 14.50 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.09400 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 21.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 10.80 REMARK 200 R MERGE FOR SHELL (I) : 0.49500 REMARK 200 R SYM FOR SHELL (I) : 0.49500 REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX AUTOMR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.88 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.41 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.15M SODIUM THIOCYANATE, 0.1M BIS REMARK 280 -TRIS, 13% PEG3350, 2% BENZAMIDINE, 2.5 MM GTP, 5 MM MNCL2, PH REMARK 280 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 12.90667 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 25.81333 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 19.36000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 32.26667 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 6.45333 REMARK 290 REMARK 290 REMARK: NULL 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 300 REMARK: MONOMER 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLN A 429 REMARK 465 PHE A 430 REMARK 465 ASN A 431 REMARK 465 GLN A 432 REMARK 465 ALA A 433 REMARK 465 PRO A 434 REMARK 465 ALA A 435 REMARK 465 ASN A 436 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU A 193 CG CD OE1 OE2 REMARK 470 PHE A 195 CG CD1 CD2 CE1 CE2 CZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT 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 OD1 ASP A 150 O HOH A 883 2.14 REMARK 500 O HOH A 792 O HOH A 935 2.17 REMARK 500 O HOH A 839 O HOH A 921 2.19 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 SER A 165 1.82 81.38 REMARK 500 ASN A 362 -83.49 -86.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 506 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 310 OD2 REMARK 620 2 ASP A 343 OD2 109.8 REMARK 620 3 GTP A 504 O1A 83.5 162.6 REMARK 620 4 GTP A 504 O2B 167.6 80.0 85.5 REMARK 620 5 HOH A 836 O 87.3 79.6 90.1 87.2 REMARK 620 6 HOH A 894 O 88.5 97.2 94.3 97.8 173.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 507 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 343 OD2 REMARK 620 2 GTP A 504 O2B 81.9 REMARK 620 3 GTP A 504 O2G 161.0 79.2 REMARK 620 4 HOH A 647 O 91.5 89.8 89.8 REMARK 620 5 HOH A 657 O 82.6 89.6 95.8 174.1 REMARK 620 6 HOH A 893 O 109.7 166.0 88.9 97.5 84.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 505 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 890 O REMARK 620 2 HOH A 891 O 95.0 REMARK 620 3 HOH A 892 O 92.8 99.0 REMARK 620 4 HOH A 899 O 88.5 84.0 176.6 REMARK 620 5 HOH A 901 O 87.4 173.8 86.6 90.4 REMARK 620 6 HOH A 903 O 169.2 95.6 83.5 94.7 82.3 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BEN A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BEN A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BEN A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GTP A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 507 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4E2K RELATED DB: PDB REMARK 900 APO SADNAG RPD REMARK 900 RELATED ID: 4EE1 RELATED DB: PDB REMARK 900 RELATED ID: 4EDG RELATED DB: PDB REMARK 900 RELATED ID: 4EDR RELATED DB: PDB REMARK 900 RELATED ID: 4EDT RELATED DB: PDB REMARK 900 RELATED ID: 4EDV RELATED DB: PDB DBREF 4EDK A 111 436 UNP O05338 PRIM_STAAU 111 436 SEQADV 4EDK SER A 108 UNP O05338 EXPRESSION TAG SEQADV 4EDK ASN A 109 UNP O05338 EXPRESSION TAG SEQADV 4EDK ALA A 110 UNP O05338 EXPRESSION TAG SEQRES 1 A 329 SER ASN ALA ASP ASP LEU GLN MET ILE GLU MET HIS GLU SEQRES 2 A 329 LEU ILE GLN GLU PHE TYR TYR TYR ALA LEU THR LYS THR SEQRES 3 A 329 VAL GLU GLY GLU GLN ALA LEU THR TYR LEU GLN GLU ARG SEQRES 4 A 329 GLY PHE THR ASP ALA LEU ILE LYS GLU ARG GLY ILE GLY SEQRES 5 A 329 PHE ALA PRO ASP SER SER HIS PHE CYS HIS ASP PHE LEU SEQRES 6 A 329 GLN LYS LYS GLY TYR ASP ILE GLU LEU ALA TYR GLU ALA SEQRES 7 A 329 GLY LEU LEU SER ARG ASN GLU GLU ASN PHE SER TYR TYR SEQRES 8 A 329 ASP ARG PHE ARG ASN ARG ILE MET PHE PRO LEU LYS ASN SEQRES 9 A 329 ALA GLN GLY ARG ILE VAL GLY TYR SER GLY ARG THR TYR SEQRES 10 A 329 THR GLY GLN GLU PRO LYS TYR LEU ASN SER PRO GLU THR SEQRES 11 A 329 PRO ILE PHE GLN LYS ARG LYS LEU LEU TYR ASN LEU ASP SEQRES 12 A 329 LYS ALA ARG LYS SER ILE ARG LYS LEU ASP GLU ILE VAL SEQRES 13 A 329 LEU LEU GLU GLY PHE MET ASP VAL ILE LYS SER ASP THR SEQRES 14 A 329 ALA GLY LEU LYS ASN VAL VAL ALA THR MET GLY THR GLN SEQRES 15 A 329 LEU SER ASP GLU HIS ILE THR PHE ILE ARG LYS LEU THR SEQRES 16 A 329 SER ASN ILE THR LEU MET PHE ASP GLY ASP PHE ALA GLY SEQRES 17 A 329 SER GLU ALA THR LEU LYS THR GLY GLN HIS LEU LEU GLN SEQRES 18 A 329 GLN GLY LEU ASN VAL PHE VAL ILE GLN LEU PRO SER GLY SEQRES 19 A 329 MET ASP PRO ASP GLU TYR ILE GLY LYS TYR GLY ASN ASP SEQRES 20 A 329 ALA PHE THR THR PHE VAL LYS ASN ASP LYS LYS SER PHE SEQRES 21 A 329 ALA HIS TYR LYS VAL SER ILE LEU LYS ASP GLU ILE ALA SEQRES 22 A 329 HIS ASN ASP LEU SER TYR GLU ARG TYR LEU LYS GLU LEU SEQRES 23 A 329 SER HIS ASP ILE SER LEU MET LYS SER SER ILE LEU GLN SEQRES 24 A 329 GLN LYS ALA ILE ASN ASP VAL ALA PRO PHE PHE ASN VAL SEQRES 25 A 329 SER PRO GLU GLN LEU ALA ASN GLU ILE GLN PHE ASN GLN SEQRES 26 A 329 ALA PRO ALA ASN HET BEN A 501 9 HET BEN A 502 9 HET BEN A 503 9 HET GTP A 504 32 HET MN A 505 1 HET MN A 506 1 HET MN A 507 1 HETNAM BEN BENZAMIDINE HETNAM GTP GUANOSINE-5'-TRIPHOSPHATE HETNAM MN MANGANESE (II) ION FORMUL 2 BEN 3(C7 H8 N2) FORMUL 5 GTP C10 H16 N5 O14 P3 FORMUL 6 MN 3(MN 2+) FORMUL 9 HOH *360(H2 O) HELIX 1 1 SER A 108 THR A 133 1 26 HELIX 2 2 GLY A 136 ARG A 146 1 11 HELIX 3 3 THR A 149 GLY A 157 1 9 HELIX 4 4 HIS A 166 LYS A 175 1 10 HELIX 5 5 ASP A 178 ALA A 185 1 8 HELIX 6 6 ASN A 248 ASP A 260 1 13 HELIX 7 7 GLY A 267 GLY A 278 1 12 HELIX 8 8 SER A 291 LYS A 300 1 10 HELIX 9 9 ASP A 312 GLN A 329 1 18 HELIX 10 10 ASP A 343 GLY A 352 1 10 HELIX 11 11 GLY A 352 ASP A 363 1 12 HELIX 12 12 PHE A 367 LEU A 375 1 9 HELIX 13 13 LEU A 375 ASN A 382 1 8 HELIX 14 14 ASN A 382 MET A 400 1 19 HELIX 15 15 SER A 402 ALA A 414 1 13 HELIX 16 16 PRO A 415 ASN A 418 5 4 HELIX 17 17 SER A 420 ILE A 428 1 9 SHEET 1 A 4 GLY A 159 ALA A 161 0 SHEET 2 A 4 ARG A 204 LYS A 210 -1 O ARG A 204 N ALA A 161 SHEET 3 A 4 ILE A 216 ARG A 222 -1 O ARG A 222 N ILE A 205 SHEET 4 A 4 TYR A 231 ASN A 233 -1 O LEU A 232 N GLY A 221 SHEET 1 B 2 LEU A 188 ARG A 190 0 SHEET 2 B 2 TYR A 197 ASP A 199 -1 O TYR A 198 N SER A 189 SHEET 1 C 5 VAL A 282 VAL A 283 0 SHEET 2 C 5 ILE A 262 LEU A 265 1 N LEU A 265 O VAL A 283 SHEET 3 C 5 ASN A 304 MET A 308 1 O THR A 306 N LEU A 264 SHEET 4 C 5 ASN A 332 ILE A 336 1 O PHE A 334 N LEU A 307 SHEET 5 C 5 LYS A 364 SER A 366 -1 O LYS A 365 N VAL A 335 LINK OD2 ASP A 310 MN MN A 506 1555 1555 2.37 LINK OD2 ASP A 343 MN MN A 506 1555 1555 2.34 LINK OD2 ASP A 343 MN MN A 507 1555 1555 2.33 LINK O1A GTP A 504 MN MN A 506 1555 1555 2.31 LINK O2B GTP A 504 MN MN A 506 1555 1555 2.32 LINK O2B GTP A 504 MN MN A 507 1555 1555 2.24 LINK O2G GTP A 504 MN MN A 507 1555 1555 2.34 LINK MN MN A 505 O HOH A 890 1555 1555 2.41 LINK MN MN A 505 O HOH A 891 1555 1555 2.42 LINK MN MN A 505 O HOH A 892 1555 1555 2.60 LINK MN MN A 505 O HOH A 899 1555 1555 2.49 LINK MN MN A 505 O HOH A 901 1555 1555 2.49 LINK MN MN A 505 O HOH A 903 1555 1555 2.59 LINK MN MN A 506 O HOH A 836 1555 1555 2.46 LINK MN MN A 506 O HOH A 894 1555 1555 2.19 LINK MN MN A 507 O HOH A 647 1555 1555 2.41 LINK MN MN A 507 O HOH A 657 1555 1555 2.44 LINK MN MN A 507 O HOH A 893 1555 1555 2.40 CISPEP 1 GLU A 228 PRO A 229 0 0.30 SITE 1 AC1 6 GLU A 117 GLU A 124 PHE A 125 VAL A 134 SITE 2 AC1 6 HOH A 747 HOH A 841 SITE 1 AC2 6 GLN A 289 LEU A 290 ASP A 292 LYS A 321 SITE 2 AC2 6 HIS A 325 HOH A 877 SITE 1 AC3 3 GLY A 287 GTP A 504 HOH A 908 SITE 1 AC4 24 ARG A 146 ARG A 222 PRO A 229 LYS A 230 SITE 2 AC4 24 TYR A 231 GLU A 266 GLY A 267 PHE A 268 SITE 3 AC4 24 MET A 269 GLY A 287 ASP A 310 ASP A 343 SITE 4 AC4 24 BEN A 503 MN A 506 MN A 507 HOH A 610 SITE 5 AC4 24 HOH A 643 HOH A 647 HOH A 658 HOH A 729 SITE 6 AC4 24 HOH A 817 HOH A 867 HOH A 899 HOH A 941 SITE 1 AC5 7 ASP A 312 HOH A 890 HOH A 891 HOH A 892 SITE 2 AC5 7 HOH A 899 HOH A 901 HOH A 903 SITE 1 AC6 6 ASP A 310 ASP A 343 GTP A 504 MN A 507 SITE 2 AC6 6 HOH A 836 HOH A 894 SITE 1 AC7 6 ASP A 343 GTP A 504 MN A 506 HOH A 647 SITE 2 AC7 6 HOH A 657 HOH A 893 CRYST1 151.742 151.742 38.720 90.00 90.00 120.00 P 61 6 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 0.006590 0.003805 0.000000 0.00000 SCALE2 0.000000 0.007610 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025826 0.00000