HEADER TRANSFERASE 27-MAR-12 4EDG TITLE THE STRUCTURE OF THE S. AUREUS DNAG RNA POLYMERASE DOMAIN BOUND TO ATP 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 13-SEP-23 4EDG 1 REMARK SEQADV LINK REVDAT 3 10-JUL-13 4EDG 1 JRNL REVDAT 2 01-AUG-12 4EDG 1 TITLE REVDAT 1 25-JUL-12 4EDG 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) : 43.67 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 34480 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) : 0.162 REMARK 3 FREE R VALUE : 0.197 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.940 REMARK 3 FREE R VALUE TEST SET COUNT : 1705 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 43.6756 - 4.5838 0.99 2857 148 0.1561 0.1752 REMARK 3 2 4.5838 - 3.6389 1.00 2787 130 0.1409 0.1681 REMARK 3 3 3.6389 - 3.1790 1.00 2723 152 0.1683 0.2050 REMARK 3 4 3.1790 - 2.8884 1.00 2757 137 0.1710 0.2125 REMARK 3 5 2.8884 - 2.6814 1.00 2715 167 0.1624 0.2083 REMARK 3 6 2.6814 - 2.5234 1.00 2734 132 0.1672 0.1941 REMARK 3 7 2.5234 - 2.3970 1.00 2687 145 0.1616 0.2066 REMARK 3 8 2.3970 - 2.2927 1.00 2711 151 0.1596 0.2018 REMARK 3 9 2.2927 - 2.2044 1.00 2725 151 0.1626 0.2207 REMARK 3 10 2.2044 - 2.1283 1.00 2709 135 0.1723 0.2253 REMARK 3 11 2.1283 - 2.0618 1.00 2705 139 0.1801 0.2105 REMARK 3 12 2.0618 - 2.0029 0.98 2665 118 0.2114 0.2658 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 : 0.33 REMARK 3 B_SOL : 46.33 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.150 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.61710 REMARK 3 B22 (A**2) : 2.61710 REMARK 3 B33 (A**2) : -5.23420 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 : 0.008 2769 REMARK 3 ANGLE : 1.062 3757 REMARK 3 CHIRALITY : 0.066 402 REMARK 3 PLANARITY : 0.004 481 REMARK 3 DIHEDRAL : 13.809 1052 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): 25.7354 -63.2181 -7.8824 REMARK 3 T TENSOR REMARK 3 T11: 0.2456 T22: 0.1576 REMARK 3 T33: 0.1082 T12: 0.1331 REMARK 3 T13: -0.0135 T23: -0.0157 REMARK 3 L TENSOR REMARK 3 L11: 1.1963 L22: 0.9999 REMARK 3 L33: 2.3865 L12: -0.4759 REMARK 3 L13: -0.3513 L23: -0.2981 REMARK 3 S TENSOR REMARK 3 S11: 0.0187 S12: 0.0499 S13: -0.0124 REMARK 3 S21: -0.0041 S22: 0.0021 S23: 0.0354 REMARK 3 S31: 0.1956 S32: -0.0638 S33: 0.0134 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 234:343) REMARK 3 ORIGIN FOR THE GROUP (A): 16.0761 -42.9050 1.6297 REMARK 3 T TENSOR REMARK 3 T11: 0.1925 T22: 0.1737 REMARK 3 T33: 0.1770 T12: 0.1049 REMARK 3 T13: -0.0368 T23: -0.0629 REMARK 3 L TENSOR REMARK 3 L11: 1.2436 L22: 3.0522 REMARK 3 L33: 0.5082 L12: -0.6434 REMARK 3 L13: -0.3493 L23: 0.2252 REMARK 3 S TENSOR REMARK 3 S11: -0.0427 S12: -0.1001 S13: 0.1516 REMARK 3 S21: 0.0479 S22: -0.0044 S23: -0.0061 REMARK 3 S31: 0.0713 S32: 0.0800 S33: -0.0143 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 344:362) REMARK 3 ORIGIN FOR THE GROUP (A): 22.2235 -32.3238 -11.2401 REMARK 3 T TENSOR REMARK 3 T11: 0.5427 T22: 0.3457 REMARK 3 T33: 0.4169 T12: 0.0323 REMARK 3 T13: 0.1010 T23: -0.0468 REMARK 3 L TENSOR REMARK 3 L11: 0.1824 L22: 0.1167 REMARK 3 L33: 0.0978 L12: 0.0300 REMARK 3 L13: -0.0123 L23: -0.0849 REMARK 3 S TENSOR REMARK 3 S11: 0.0609 S12: 0.3506 S13: 0.2671 REMARK 3 S21: -0.5107 S22: 0.0641 S23: -0.2729 REMARK 3 S31: -0.4726 S32: 0.4190 S33: 0.0001 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 363:428) REMARK 3 ORIGIN FOR THE GROUP (A): -0.6938 -25.2772 3.7241 REMARK 3 T TENSOR REMARK 3 T11: 0.1950 T22: 0.1594 REMARK 3 T33: 0.3283 T12: 0.0386 REMARK 3 T13: -0.0102 T23: -0.0487 REMARK 3 L TENSOR REMARK 3 L11: 1.8798 L22: 1.4876 REMARK 3 L33: 0.8225 L12: 0.1567 REMARK 3 L13: 0.2062 L23: -0.5520 REMARK 3 S TENSOR REMARK 3 S11: 0.0177 S12: -0.1896 S13: 0.2487 REMARK 3 S21: 0.1032 S22: 0.0333 S23: 0.1156 REMARK 3 S31: -0.0177 S32: -0.0569 S33: -0.0006 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 4EDG 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_1000071478. 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 3.3.20 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34499 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.003 REMARK 200 RESOLUTION RANGE LOW (A) : 130.996 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 5.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04600 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 22.1000 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 (%) : 98.8 REMARK 200 DATA REDUNDANCY IN SHELL : 5.30 REMARK 200 R MERGE FOR SHELL (I) : 0.28700 REMARK 200 R SYM FOR SHELL (I) : 0.28700 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.800 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: PDB ENTRY 4E2K REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.60 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 ATP, 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 12.88833 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 25.77667 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 19.33250 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 32.22083 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 6.44417 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 470 GLN A 407 CG CD OE1 NE2 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 O2' ATP A 503 O HOH A 847 2.18 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 2.54 82.59 REMARK 500 HIS A 166 17.19 -141.75 REMARK 500 ASN A 248 -0.09 80.36 REMARK 500 ASN A 281 51.05 -93.43 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 504 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 310 OD2 REMARK 620 2 ASP A 343 OD2 111.3 REMARK 620 3 ATP A 503 O2A 84.5 160.2 REMARK 620 4 ATP A 503 O2B 152.9 89.1 72.4 REMARK 620 5 ATP A 503 O2B 150.2 89.0 72.0 4.1 REMARK 620 6 ATP A 503 O2A 88.7 159.7 16.2 73.1 74.0 REMARK 620 7 HOH A 760 O 85.0 81.9 88.0 80.4 76.3 104.0 REMARK 620 8 HOH A 829 O 85.8 102.2 90.4 107.8 111.8 75.1 170.8 REMARK 620 N 1 2 3 4 5 6 7 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 343 OD2 REMARK 620 2 ATP A 503 O3G 167.3 REMARK 620 3 ATP A 503 O3G 162.3 5.5 REMARK 620 4 ATP A 503 O2B 86.4 80.9 75.9 REMARK 620 5 ATP A 503 O2B 86.1 81.4 76.2 4.0 REMARK 620 6 HOH A 781 O 91.7 88.6 91.5 99.3 103.3 REMARK 620 7 HOH A 782 O 102.9 89.7 94.2 163.7 160.5 93.8 REMARK 620 8 HOH A 793 O 77.8 101.2 98.0 78.4 74.5 169.3 90.5 REMARK 620 N 1 2 3 4 5 6 7 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 HOH A 776 O REMARK 620 2 HOH A 849 O 108.9 REMARK 620 3 HOH A 902 O 87.9 108.5 REMARK 620 N 1 2 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 ATP 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 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 506 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4E2K RELATED DB: PDB REMARK 900 APO PROTEIN REMARK 900 RELATED ID: 4EDK 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 REMARK 900 RELATED ID: 4EE1 RELATED DB: PDB DBREF 4EDG A 111 436 UNP O05338 PRIM_STAAU 111 436 SEQADV 4EDG SER A 108 UNP O05338 EXPRESSION TAG SEQADV 4EDG ASN A 109 UNP O05338 EXPRESSION TAG SEQADV 4EDG 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 ATP A 503 62 HET MN A 504 1 HET MN A 505 1 HET MN A 506 1 HETNAM BEN BENZAMIDINE HETNAM ATP ADENOSINE-5'-TRIPHOSPHATE HETNAM MN MANGANESE (II) ION FORMUL 2 BEN 2(C7 H8 N2) FORMUL 4 ATP C10 H16 N5 O13 P3 FORMUL 5 MN 3(MN 2+) FORMUL 8 HOH *350(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 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 LEU A 264 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 504 1555 1555 2.48 LINK OD2 ASP A 343 MN MN A 504 1555 1555 2.32 LINK OD2 ASP A 343 MN MN A 505 1555 1555 2.35 LINK O2ABATP A 503 MN MN A 504 1555 1555 2.42 LINK O2BAATP A 503 MN MN A 504 1555 1555 2.45 LINK O2BBATP A 503 MN MN A 504 1555 1555 2.47 LINK O2AAATP A 503 MN MN A 504 1555 1555 2.48 LINK O3GAATP A 503 MN MN A 505 1555 1555 2.37 LINK O3GBATP A 503 MN MN A 505 1555 1555 2.38 LINK O2BAATP A 503 MN MN A 505 1555 1555 2.53 LINK O2BBATP A 503 MN MN A 505 1555 1555 2.56 LINK MN MN A 504 O HOH A 760 1555 1555 2.52 LINK MN MN A 504 O HOH A 829 1555 1555 2.31 LINK MN MN A 505 O HOH A 781 1555 1555 2.41 LINK MN MN A 505 O HOH A 782 1555 1555 2.38 LINK MN MN A 505 O HOH A 793 1555 1555 2.43 LINK MN MN A 506 O HOH A 776 1555 1555 2.48 LINK MN MN A 506 O HOH A 849 1555 1555 2.53 LINK MN MN A 506 O HOH A 902 1555 1555 1.95 CISPEP 1 GLU A 228 PRO A 229 0 -2.56 SITE 1 AC1 6 GLU A 117 PHE A 125 TYR A 128 VAL A 134 SITE 2 AC1 6 HOH A 694 HOH A 753 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 789 SITE 1 AC3 25 ARG A 146 ARG A 222 PRO A 229 LYS A 230 SITE 2 AC3 25 TYR A 231 GLU A 266 GLY A 267 PHE A 268 SITE 3 AC3 25 MET A 269 GLY A 287 ASP A 310 ASP A 343 SITE 4 AC3 25 MN A 504 MN A 505 HOH A 620 HOH A 656 SITE 5 AC3 25 HOH A 704 HOH A 760 HOH A 781 HOH A 793 SITE 6 AC3 25 HOH A 811 HOH A 829 HOH A 847 HOH A 866 SITE 7 AC3 25 HOH A 902 SITE 1 AC4 6 ASP A 310 ASP A 343 ATP A 503 MN A 505 SITE 2 AC4 6 HOH A 760 HOH A 829 SITE 1 AC5 6 ASP A 343 ATP A 503 MN A 504 HOH A 781 SITE 2 AC5 6 HOH A 782 HOH A 793 SITE 1 AC6 5 ASP A 310 ASP A 312 HOH A 776 HOH A 849 SITE 2 AC6 5 HOH A 902 CRYST1 151.261 151.261 38.665 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 0.006611 0.003817 0.000000 0.00000 SCALE2 0.000000 0.007634 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025863 0.00000