HEADER TRANSFERASE/TRANSFERASE INHIBITOR 27-MAR-12 4EDV TITLE THE STRUCTURE OF THE S. AUREUS DNAG RNA POLYMERASE DOMAIN BOUND TO TITLE 2 PPPGPP 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, BACTERIAL, NUCLEOTIDE, NUCLEOSIDE TRIPHOSPHATE, KEYWDS 2 NUCLEOSIDE POLYPHOSPHATE, PROTEIN-LIGAND COMPLEX, TRANSFERASE, KEYWDS 3 TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR R.U.RYMER,F.A.SOLORIO,C.CHU,J.E.CORN,J.D.WANG,J.M.BERGER REVDAT 5 28-FEB-24 4EDV 1 REMARK SEQADV LINK REVDAT 4 12-NOV-14 4EDV 1 HETATM REVDAT 3 10-JUL-13 4EDV 1 JRNL REVDAT 2 01-AUG-12 4EDV 1 TITLE REVDAT 1 25-JUL-12 4EDV 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. 2.01 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) : 2.01 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.11 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.460 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 34198 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.169 REMARK 3 R VALUE (WORKING SET) : 0.167 REMARK 3 FREE R VALUE : 0.203 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.090 REMARK 3 FREE R VALUE TEST SET COUNT : 1739 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 37.1143 - 4.5992 0.99 2815 144 0.1676 0.1882 REMARK 3 2 4.5992 - 3.6515 1.00 2770 134 0.1405 0.1635 REMARK 3 3 3.6515 - 3.1902 1.00 2703 147 0.1667 0.2041 REMARK 3 4 3.1902 - 2.8987 1.00 2734 137 0.1731 0.2204 REMARK 3 5 2.8987 - 2.6910 1.00 2670 164 0.1714 0.2235 REMARK 3 6 2.6910 - 2.5324 1.00 2713 131 0.1745 0.2287 REMARK 3 7 2.5324 - 2.4056 1.00 2667 138 0.1616 0.1993 REMARK 3 8 2.4056 - 2.3009 1.00 2688 154 0.1693 0.1946 REMARK 3 9 2.3009 - 2.2123 1.00 2688 156 0.1668 0.2093 REMARK 3 10 2.2123 - 2.1360 1.00 2660 125 0.1825 0.2412 REMARK 3 11 2.1360 - 2.0692 1.00 2692 164 0.1990 0.2210 REMARK 3 12 2.0692 - 2.0100 1.00 2659 145 0.2395 0.3222 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.30 REMARK 3 SHRINKAGE RADIUS : 1.11 REMARK 3 K_SOL : 0.32 REMARK 3 B_SOL : 40.18 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.470 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 31.06 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.37 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.54700 REMARK 3 B22 (A**2) : 3.54700 REMARK 3 B33 (A**2) : -7.09410 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 : 0.003 2720 REMARK 3 ANGLE : 0.720 3679 REMARK 3 CHIRALITY : 0.052 394 REMARK 3 PLANARITY : 0.003 471 REMARK 3 DIHEDRAL : 13.744 1040 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): 143.2749 121.5898 -3.3855 REMARK 3 T TENSOR REMARK 3 T11: 0.1039 T22: 0.4708 REMARK 3 T33: 0.1524 T12: -0.0308 REMARK 3 T13: -0.0004 T23: -0.0151 REMARK 3 L TENSOR REMARK 3 L11: 1.9217 L22: 0.5399 REMARK 3 L33: 2.2019 L12: 0.0277 REMARK 3 L13: -0.0646 L23: -0.2983 REMARK 3 S TENSOR REMARK 3 S11: -0.0191 S12: 0.0671 S13: -0.0711 REMARK 3 S21: -0.0316 S22: 0.0306 S23: -0.0215 REMARK 3 S31: 0.1689 S32: 0.1875 S33: 0.0150 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 234:343) REMARK 3 ORIGIN FOR THE GROUP (A): 121.0324 123.7166 6.2889 REMARK 3 T TENSOR REMARK 3 T11: 0.0825 T22: 0.3403 REMARK 3 T33: 0.2072 T12: -0.0336 REMARK 3 T13: 0.0339 T23: -0.0354 REMARK 3 L TENSOR REMARK 3 L11: 3.5189 L22: 1.3488 REMARK 3 L33: 0.7143 L12: -0.6506 REMARK 3 L13: -0.3527 L23: -0.1678 REMARK 3 S TENSOR REMARK 3 S11: 0.0034 S12: -0.1080 S13: 0.0155 REMARK 3 S21: 0.0728 S22: 0.0181 S23: 0.1369 REMARK 3 S31: -0.0132 S32: 0.1243 S33: -0.0052 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 344:362) REMARK 3 ORIGIN FOR THE GROUP (A): 115.0045 134.2569 -6.6382 REMARK 3 T TENSOR REMARK 3 T11: 0.3418 T22: 0.5864 REMARK 3 T33: 0.4330 T12: 0.0463 REMARK 3 T13: 0.0633 T23: 0.0804 REMARK 3 L TENSOR REMARK 3 L11: 0.2863 L22: 0.3492 REMARK 3 L33: 0.6939 L12: 0.1346 REMARK 3 L13: 0.1249 L23: 0.0340 REMARK 3 S TENSOR REMARK 3 S11: 0.0329 S12: 0.6101 S13: 0.1014 REMARK 3 S21: -0.4369 S22: -0.2105 S23: 0.1194 REMARK 3 S31: -0.6959 S32: -0.3069 S33: -0.0119 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 363:428) REMARK 3 ORIGIN FOR THE GROUP (A): 97.2101 118.0214 8.6388 REMARK 3 T TENSOR REMARK 3 T11: 0.1562 T22: 0.2484 REMARK 3 T33: 0.3817 T12: 0.0191 REMARK 3 T13: 0.0504 T23: -0.0085 REMARK 3 L TENSOR REMARK 3 L11: 1.6481 L22: 2.3593 REMARK 3 L33: 1.1125 L12: 0.6475 REMARK 3 L13: 0.5190 L23: -0.1207 REMARK 3 S TENSOR REMARK 3 S11: 0.0620 S12: -0.1553 S13: 0.0008 REMARK 3 S21: 0.0802 S22: -0.0517 S23: 0.1346 REMARK 3 S31: 0.0312 S32: -0.0667 S33: -0.0003 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 4EDV 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_1000071493. 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 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34211 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.010 REMARK 200 RESOLUTION RANGE LOW (A) : 131.059 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 8.100 REMARK 200 R MERGE (I) : 0.08300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.01 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.12 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 8.20 REMARK 200 R MERGE FOR SHELL (I) : 0.57200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.300 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 (%): 63.66 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.38 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.15M SODIUM THIOCYANATE, 0.1M BIS REMARK 280 -TRIS, 13% PEG3350, 2% BENZAMIDINE, 2.5 MM PPPGPP, 10 MM MNCL2, REMARK 280 1 MM MGCL2, PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 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 12.89700 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 25.79400 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 19.34550 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 32.24250 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 6.44850 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 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 O HOH A 708 O HOH A 799 2.09 REMARK 500 OD2 ASP A 270 O HOH A 709 2.18 REMARK 500 O HOH A 704 O HOH A 888 2.19 REMARK 500 OD2 ASP A 310 O HOH A 711 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 HIS A 166 18.30 -142.45 REMARK 500 ASN A 248 -0.68 79.22 REMARK 500 ASN A 281 48.97 -91.77 REMARK 500 ASN A 362 -77.87 -77.81 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 503 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 310 OD2 REMARK 620 2 ASP A 343 OD2 109.1 REMARK 620 3 0O2 A 502 O2A 81.7 166.9 REMARK 620 4 0O2 A 502 O1B 150.7 91.7 75.6 REMARK 620 5 HOH A 708 O 90.4 72.6 100.5 75.9 REMARK 620 6 HOH A 709 O 86.5 103.3 84.4 109.2 173.8 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 ASP A 312 OD2 REMARK 620 2 0O2 A 502 O1C 85.5 REMARK 620 3 0O2 A 502 O2D 133.6 97.2 REMARK 620 4 HOH A 692 O 88.5 164.3 76.5 REMARK 620 5 HOH A 706 O 139.8 113.1 81.3 80.5 REMARK 620 6 HOH A 711 O 67.6 86.2 158.6 105.0 78.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 504 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 343 OD2 REMARK 620 2 0O2 A 502 O3G 170.8 REMARK 620 3 0O2 A 502 O1B 92.5 78.9 REMARK 620 4 HOH A 611 O 90.1 88.9 104.1 REMARK 620 5 HOH A 712 O 92.8 96.3 165.9 88.9 REMARK 620 6 HOH A 799 O 74.5 106.6 78.9 164.5 89.9 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 0O2 A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN 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 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: 4EDZ RELATED DB: PDB REMARK 900 RELATED ID: 4EDY RELATED DB: PDB REMARK 900 RELATED ID: 4EDT RELATED DB: PDB REMARK 900 RELATED ID: 4EDR RELATED DB: PDB DBREF 4EDV A 111 436 UNP O05338 PRIM_STAAU 111 436 SEQADV 4EDV SER A 108 UNP O05338 EXPRESSION TAG SEQADV 4EDV ASN A 109 UNP O05338 EXPRESSION TAG SEQADV 4EDV 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 0O2 A 502 40 HET MN A 503 1 HET MN A 504 1 HET MN A 505 1 HETNAM BEN BENZAMIDINE HETNAM 0O2 GUANOSINE 5'-(TETRAHYDROGEN TRIPHOSPHATE) 3'- HETNAM 2 0O2 (TRIHYDROGEN DIPHOSPHATE) HETNAM MN MANGANESE (II) ION FORMUL 2 BEN C7 H8 N2 FORMUL 3 0O2 C10 H18 N5 O20 P5 FORMUL 4 MN 3(MN 2+) FORMUL 7 HOH *299(H2 O) HELIX 1 1 SER A 108 LYS A 132 1 25 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 THR A 302 1 12 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 ASN A 191 0 SHEET 2 B 2 SER A 196 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 264 1 N VAL A 263 O VAL A 283 SHEET 3 C 5 ASN A 304 LEU A 307 1 O THR A 306 N ILE A 262 SHEET 4 C 5 ASN A 332 VAL A 335 1 O PHE A 334 N LEU A 307 SHEET 5 C 5 LYS A 365 SER A 366 -1 O LYS A 365 N VAL A 335 LINK OD2 ASP A 310 MN MN A 503 1555 1555 2.47 LINK OD2 ASP A 312 MN MN A 505 1555 1555 2.57 LINK OD2 ASP A 343 MN MN A 503 1555 1555 2.45 LINK OD2 ASP A 343 MN MN A 504 1555 1555 2.42 LINK O2A 0O2 A 502 MN MN A 503 1555 1555 2.45 LINK O1B 0O2 A 502 MN MN A 503 1555 1555 2.48 LINK O3G 0O2 A 502 MN MN A 504 1555 1555 2.46 LINK O1B 0O2 A 502 MN MN A 504 1555 1555 2.48 LINK O1C 0O2 A 502 MN MN A 505 1555 1555 2.65 LINK O2D 0O2 A 502 MN MN A 505 1555 1555 2.73 LINK MN MN A 503 O HOH A 708 1555 1555 2.68 LINK MN MN A 503 O HOH A 709 1555 1555 2.42 LINK MN MN A 504 O HOH A 611 1555 1555 2.53 LINK MN MN A 504 O HOH A 712 1555 1555 2.49 LINK MN MN A 504 O HOH A 799 1555 1555 2.56 LINK MN MN A 505 O HOH A 692 1555 1555 2.55 LINK MN MN A 505 O HOH A 706 1555 1555 2.56 LINK MN MN A 505 O HOH A 711 1555 1555 2.62 CISPEP 1 GLU A 228 PRO A 229 0 -2.68 SITE 1 AC1 4 GLU A 124 PHE A 125 TYR A 128 HOH A 672 SITE 1 AC2 22 ARG A 146 ARG A 222 GLU A 228 PRO A 229 SITE 2 AC2 22 LYS A 230 TYR A 231 ASP A 310 ASP A 312 SITE 3 AC2 22 ALA A 314 ASP A 343 MN A 503 MN A 504 SITE 4 AC2 22 MN A 505 HOH A 611 HOH A 639 HOH A 706 SITE 5 AC2 22 HOH A 719 HOH A 751 HOH A 798 HOH A 826 SITE 6 AC2 22 HOH A 828 HOH A 829 SITE 1 AC3 6 ASP A 310 ASP A 343 0O2 A 502 MN A 504 SITE 2 AC3 6 HOH A 708 HOH A 709 SITE 1 AC4 6 ASP A 343 0O2 A 502 MN A 503 HOH A 611 SITE 2 AC4 6 HOH A 712 HOH A 799 SITE 1 AC5 5 ASP A 312 0O2 A 502 HOH A 692 HOH A 706 SITE 2 AC5 5 HOH A 711 CRYST1 151.334 151.334 38.691 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 0.006608 0.003815 0.000000 0.00000 SCALE2 0.000000 0.007630 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025846 0.00000