HEADER TRANSFERASE 09-JAN-12 3VES TITLE CRYSTAL STRUCTURE OF THE O-CARBAMOYLTRANSFERASE TOBZ IN COMPLEX WITH TITLE 2 AMPCPP AND CARBAMOYL PHOSPHATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: O-CARBAMOYLTRANSFERASE TOBZ; COMPND 3 CHAIN: A; COMPND 4 EC: 2.1.3.-; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOALLOTEICHUS TENEBRARIUS; SOURCE 3 ORGANISM_COMMON: STREPTOMYCES TENEBRARIUS; SOURCE 4 ORGANISM_TAXID: 1933; SOURCE 5 STRAIN: DSM40770T; SOURCE 6 GENE: TACA, TOBZ; SOURCE 7 EXPRESSION_SYSTEM: STREPTOMYCES LIVIDANS; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 457428; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: TK24; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PUWL201PW KEYWDS ANTIBIOTIC BIOSYNTHESIS, SUBSTRATE ASSISTED CATALYSIS, SUBSTRATE KEYWDS 2 CHANNELING, ADENYLATION, STRUCTURAL ENZYMOLOGY, ENZYME EVOLUTION, KEYWDS 3 TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR C.PARTHIER,M.T.STUBBS,S.GOERLICH,F.JAENECKE REVDAT 5 13-SEP-23 3VES 1 REMARK SEQADV LINK REVDAT 4 15-NOV-17 3VES 1 REMARK REVDAT 3 02-MAY-12 3VES 1 JRNL REVDAT 2 14-MAR-12 3VES 1 JRNL REVDAT 1 25-JAN-12 3VES 0 JRNL AUTH C.PARTHIER,S.GORLICH,F.JAENECKE,C.BREITHAUPT,U.BRAUER, JRNL AUTH 2 U.FANDRICH,D.CLAUSNITZER,U.F.WEHMEIER,C.BOTTCHER,D.SCHEEL, JRNL AUTH 3 M.T.STUBBS JRNL TITL THE O-CARBAMOYLTRANSFERASE TOBZ CATALYZES AN ANCIENT JRNL TITL 2 ENZYMATIC REACTION. JRNL REF ANGEW.CHEM.INT.ED.ENGL. V. 51 4046 2012 JRNL REFN ISSN 1433-7851 JRNL PMID 22383337 JRNL DOI 10.1002/ANIE.201108896 REMARK 2 REMARK 2 RESOLUTION. 2.23 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.7.2_869 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) : 2.23 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.98 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.990 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 40443 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.232 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2023 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 33.9879 - 5.3681 1.00 3035 160 0.1751 0.2038 REMARK 3 2 5.3681 - 4.2635 1.00 2819 149 0.1471 0.1648 REMARK 3 3 4.2635 - 3.7253 1.00 2790 146 0.1515 0.1973 REMARK 3 4 3.7253 - 3.3851 1.00 2758 146 0.1775 0.2389 REMARK 3 5 3.3851 - 3.1426 1.00 2745 144 0.1890 0.2192 REMARK 3 6 3.1426 - 2.9574 1.00 2717 143 0.1843 0.2563 REMARK 3 7 2.9574 - 2.8094 1.00 2723 143 0.1872 0.2533 REMARK 3 8 2.8094 - 2.6872 1.00 2711 143 0.1931 0.2795 REMARK 3 9 2.6872 - 2.5838 1.00 2702 142 0.2025 0.2769 REMARK 3 10 2.5838 - 2.4946 1.00 2697 142 0.2107 0.3010 REMARK 3 11 2.4946 - 2.4166 1.00 2686 142 0.2217 0.2888 REMARK 3 12 2.4166 - 2.3476 1.00 2677 140 0.2340 0.3095 REMARK 3 13 2.3476 - 2.2858 1.00 2674 141 0.2354 0.2911 REMARK 3 14 2.2858 - 2.2300 0.99 2686 142 0.2568 0.2862 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 : 0.34 REMARK 3 B_SOL : 29.66 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.540 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.670 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 38.06 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.17 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.97340 REMARK 3 B22 (A**2) : 2.97340 REMARK 3 B33 (A**2) : -5.94680 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 4568 REMARK 3 ANGLE : 1.066 6235 REMARK 3 CHIRALITY : 0.070 678 REMARK 3 PLANARITY : 0.004 823 REMARK 3 DIHEDRAL : 14.929 1655 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 0:151) REMARK 3 ORIGIN FOR THE GROUP (A): 11.9360 32.2836 26.4161 REMARK 3 T TENSOR REMARK 3 T11: 0.1559 T22: 0.1261 REMARK 3 T33: 0.1557 T12: 0.0559 REMARK 3 T13: 0.0009 T23: -0.0194 REMARK 3 L TENSOR REMARK 3 L11: 1.1690 L22: 0.4648 REMARK 3 L33: 1.7943 L12: -0.1420 REMARK 3 L13: 0.0866 L23: 0.1358 REMARK 3 S TENSOR REMARK 3 S11: 0.0008 S12: -0.0220 S13: -0.0178 REMARK 3 S21: -0.0590 S22: -0.0673 S23: 0.1274 REMARK 3 S31: -0.0345 S32: -0.1597 S33: 0.0321 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 152:300) REMARK 3 ORIGIN FOR THE GROUP (A): 16.9634 26.5096 0.5238 REMARK 3 T TENSOR REMARK 3 T11: 0.2757 T22: 0.1724 REMARK 3 T33: 0.1423 T12: 0.0634 REMARK 3 T13: -0.0509 T23: -0.0236 REMARK 3 L TENSOR REMARK 3 L11: 1.2864 L22: 0.9112 REMARK 3 L33: 0.5240 L12: -0.7767 REMARK 3 L13: 0.0582 L23: 0.0789 REMARK 3 S TENSOR REMARK 3 S11: 0.0953 S12: 0.0866 S13: -0.0694 REMARK 3 S21: -0.2647 S22: -0.0956 S23: 0.1271 REMARK 3 S31: -0.0517 S32: -0.1692 S33: 0.0002 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 301:452) REMARK 3 ORIGIN FOR THE GROUP (A): 29.9871 41.7587 16.8395 REMARK 3 T TENSOR REMARK 3 T11: 0.2069 T22: 0.1102 REMARK 3 T33: 0.1409 T12: 0.0083 REMARK 3 T13: 0.0428 T23: 0.0121 REMARK 3 L TENSOR REMARK 3 L11: 1.4075 L22: 0.7303 REMARK 3 L33: 1.2886 L12: 0.4345 REMARK 3 L13: -0.0732 L23: 0.1574 REMARK 3 S TENSOR REMARK 3 S11: -0.0431 S12: -0.1097 S13: 0.0719 REMARK 3 S21: -0.1912 S22: 0.0375 S23: -0.0908 REMARK 3 S31: -0.3411 S32: 0.1925 S33: -0.0023 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 453:566) REMARK 3 ORIGIN FOR THE GROUP (A): 35.9847 45.6613 12.7104 REMARK 3 T TENSOR REMARK 3 T11: 0.2863 T22: 0.1917 REMARK 3 T33: 0.1996 T12: -0.0592 REMARK 3 T13: 0.0537 T23: 0.0171 REMARK 3 L TENSOR REMARK 3 L11: 2.7403 L22: 1.1949 REMARK 3 L33: 1.6776 L12: 0.3247 REMARK 3 L13: -0.0157 L23: -0.3553 REMARK 3 S TENSOR REMARK 3 S11: -0.0304 S12: 0.2498 S13: 0.3514 REMARK 3 S21: -0.3505 S22: 0.0166 S23: -0.0260 REMARK 3 S31: -0.2444 S32: 0.2403 S33: -0.0126 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 3VES COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-JAN-12. REMARK 100 THE DEPOSITION ID IS D_1000069954. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-OCT-10 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 : BESSY REMARK 200 BEAMLINE : 14.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9184 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-225 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 40445 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.230 REMARK 200 RESOLUTION RANGE LOW (A) : 33.984 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 4.700 REMARK 200 R MERGE (I) : 0.09500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.9900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.23 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.29 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.78400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.370 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 3VEN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.56 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.12 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.6 M SODIUM POTASSIUM TARTRATE, 0.1 M REMARK 280 MES, PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 2 2 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 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+5/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-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 93.69967 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 187.39933 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 140.54950 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 234.24917 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 46.84983 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 93.69967 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 187.39933 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 234.24917 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 140.54950 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 46.84983 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 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 819 LIES ON A SPECIAL POSITION. 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 HIS A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 HIS A -1 REMARK 465 ASP A 567 REMARK 465 LEU A 568 REMARK 465 ARG A 569 REMARK 465 HIS A 570 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 40 -4.71 82.40 REMARK 500 GLU A 142 -49.43 -132.57 REMARK 500 ALA A 204 -55.29 -132.71 REMARK 500 LEU A 487 54.44 -118.17 REMARK 500 TRP A 495 18.54 55.82 REMARK 500 ASN A 507 79.68 -163.52 REMARK 500 ASN A 532 154.08 177.98 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 FE2 A 605 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 114 NE2 REMARK 620 2 HIS A 118 NE2 91.4 REMARK 620 3 ASP A 137 OD2 98.5 101.8 REMARK 620 4 ASP A 137 OD1 153.1 96.8 54.8 REMARK 620 5 ASP A 338 OD2 92.3 83.0 168.0 114.0 REMARK 620 6 HOH A 815 O 89.5 173.7 84.2 85.1 90.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 603 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 530 OG REMARK 620 2 CP A 601 O2P 76.4 REMARK 620 3 APC A 602 O2G 74.2 100.6 REMARK 620 4 APC A 602 O2B 146.3 132.8 82.6 REMARK 620 5 HOH A 701 O 91.5 162.7 87.7 63.0 REMARK 620 6 HOH A 702 O 87.2 74.6 161.4 114.1 92.7 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 CP A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE APC A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE2 A 605 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 606 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3VEN RELATED DB: PDB REMARK 900 TOBZ REMARK 900 RELATED ID: 3VEO RELATED DB: PDB REMARK 900 TOBZ IN COMPLEX WITH CARBAMOYL PHOSPHATE REMARK 900 RELATED ID: 3VER RELATED DB: PDB REMARK 900 TOBZ IN COMPLEX WITH CARBAMOYL ADENYLATE INTERMEDIATE REMARK 900 RELATED ID: 3VET RELATED DB: PDB REMARK 900 TOBZ IN COMPLEX WITH TOBRAMYCIN, CARBAMOYL PHOSPHATE AND ADP REMARK 900 RELATED ID: 3VEW RELATED DB: PDB REMARK 900 TOBZ IN COMPLEX WITH ADP REMARK 900 RELATED ID: 3VEX RELATED DB: PDB REMARK 900 TOBZ H14N VARIANT IN COMPLEX WITH CARBAMOYL ADENYLATE INTERMEDIATE REMARK 900 RELATED ID: 3VEZ RELATED DB: PDB REMARK 900 TOBZ K443A VARIANT IN COMPLEX WITH ATP, ADP AND CARBAMOYL PHOSPHATE REMARK 900 RELATED ID: 3VF2 RELATED DB: PDB REMARK 900 TOBZ M473I VARIANT IN COMPLEX WITH CARBAMOYL PHOSPHATE AND ADP REMARK 900 RELATED ID: 3VF4 RELATED DB: PDB REMARK 900 TOBZ S530A VARIANT IN COMPLEX WITH CARBAMOYL PHOSPHATE AND ADP DBREF 3VES A 1 570 UNP Q70IY1 Q70IY1_STRSD 1 570 SEQADV 3VES HIS A -5 UNP Q70IY1 EXPRESSION TAG SEQADV 3VES HIS A -4 UNP Q70IY1 EXPRESSION TAG SEQADV 3VES HIS A -3 UNP Q70IY1 EXPRESSION TAG SEQADV 3VES HIS A -2 UNP Q70IY1 EXPRESSION TAG SEQADV 3VES HIS A -1 UNP Q70IY1 EXPRESSION TAG SEQADV 3VES HIS A 0 UNP Q70IY1 EXPRESSION TAG SEQADV 3VES LEU A 35 UNP Q70IY1 PHE 35 ENGINEERED MUTATION SEQRES 1 A 576 HIS HIS HIS HIS HIS HIS MET ARG VAL LEU GLY LEU ASN SEQRES 2 A 576 GLY TRP PRO ARG ASP PHE HIS ASP ALA SER ALA ALA LEU SEQRES 3 A 576 LEU VAL ASP GLY ARG ILE ALA ALA PHE ALA GLU GLU GLU SEQRES 4 A 576 ARG LEU THR ARG LYS LYS HIS GLY TYR ASN THR ALA PRO SEQRES 5 A 576 VAL GLN ALA ALA ALA PHE CYS LEU ALA GLN ALA GLY LEU SEQRES 6 A 576 THR VAL ASP ASP LEU ASP ALA VAL ALA PHE GLY TRP ASP SEQRES 7 A 576 LEU PRO ALA MET TYR ARG GLU ARG LEU GLY GLY TRP PRO SEQRES 8 A 576 HIS SER ASP SER GLU ALA LEU ASP ILE LEU LEU PRO ARG SEQRES 9 A 576 ASP VAL PHE PRO ARG ARG THR ASP PRO PRO LEU HIS PHE SEQRES 10 A 576 VAL GLN HIS HIS LEU ALA HIS ALA ALA SER ALA TYR TYR SEQRES 11 A 576 PHE SER GLY GLU ASP ARG GLY ALA VAL LEU ILE VAL ASP SEQRES 12 A 576 GLY GLN GLY GLU GLU GLU CYS VAL THR LEU ALA HIS ALA SEQRES 13 A 576 GLU GLY GLY LYS ILE THR VAL LEU ASP THR VAL PRO GLY SEQRES 14 A 576 ALA TRP SER LEU GLY PHE PHE TYR GLU HIS VAL SER GLU SEQRES 15 A 576 TYR THR GLY LEU GLY GLY ASP ASN PRO GLY LYS LEU MET SEQRES 16 A 576 GLY LEU ALA ALA HIS GLY THR THR VAL ASP GLU THR LEU SEQRES 17 A 576 SER ALA PHE ALA PHE ASP SER ASP GLY TYR ARG LEU ASN SEQRES 18 A 576 LEU ILE ASP PRO GLN ALA ARG ASP PRO GLU ASP TRP ASP SEQRES 19 A 576 GLU TYR SER VAL THR GLU ARG ALA TRP PHE ALA HIS LEU SEQRES 20 A 576 GLU ARG ILE TYR ARG LEU PRO PRO ASN GLU PHE VAL ARG SEQRES 21 A 576 ARG TYR ASP PRO ALA LYS GLY ARG VAL VAL ARG ASP THR SEQRES 22 A 576 ARG ARG ASP PRO TYR GLU TYR ARG ASP LEU ALA ALA THR SEQRES 23 A 576 ALA GLN ALA ALA LEU GLU ARG ALA VAL PHE GLY LEU ALA SEQRES 24 A 576 ASP SER VAL LEU ALA ARG THR GLY GLU ARG THR LEU PHE SEQRES 25 A 576 VAL ALA GLY GLY VAL GLY LEU ASN ALA THR MET ASN GLY SEQRES 26 A 576 LYS LEU LEU THR ARG SER THR VAL ASP LYS MET PHE VAL SEQRES 27 A 576 PRO PRO VAL ALA SER ASP ILE GLY VAL SER LEU GLY ALA SEQRES 28 A 576 ALA ALA ALA VAL ALA VAL GLU LEU GLY ASP ARG ILE ALA SEQRES 29 A 576 PRO MET GLY ASP THR ALA ALA TRP GLY PRO GLU PHE SER SEQRES 30 A 576 PRO ASP GLN VAL ARG ALA ALA LEU ASP ARG THR GLY LEU SEQRES 31 A 576 ALA TYR ARG GLU PRO ALA ASN LEU GLU ARG GLU VAL ALA SEQRES 32 A 576 ALA LEU ILE ALA SER GLY LYS VAL VAL GLY TRP ALA GLN SEQRES 33 A 576 GLY ARG GLY GLU VAL GLY PRO ARG ALA LEU GLY GLN ARG SEQRES 34 A 576 SER LEU LEU GLY SER ALA HIS SER PRO THR MET ARG ASP SEQRES 35 A 576 HIS ILE ASN LEU ARG VAL LYS ASP ARG GLU TRP TRP ARG SEQRES 36 A 576 PRO PHE ALA PRO SER MET LEU ARG SER VAL SER ASP GLN SEQRES 37 A 576 VAL LEU GLU VAL ASP ALA ASP PHE PRO TYR MET ILE MET SEQRES 38 A 576 THR THR LYS VAL ARG ALA ALA TYR ALA GLU ARG LEU PRO SEQRES 39 A 576 SER VAL VAL HIS GLU ASP TRP SER THR ARG PRO GLN THR SEQRES 40 A 576 VAL THR GLU ALA SER ASN PRO ARG TYR HIS ARG MET LEU SEQRES 41 A 576 THR GLU LEU GLY ASP LEU VAL GLY ASP PRO VAL CYS LEU SEQRES 42 A 576 ASN THR SER PHE ASN ASP ARG GLY GLU PRO ILE VAL SER SEQRES 43 A 576 SER PRO ALA ASP ALA LEU LEU THR PHE SER ARG LEU PRO SEQRES 44 A 576 ILE ASP ALA LEU ALA VAL GLY PRO TYR LEU VAL THR LYS SEQRES 45 A 576 ASP LEU ARG HIS HET CP A 601 8 HET APC A 602 31 HET MN A 603 1 HET K A 604 1 HET FE2 A 605 1 HET EDO A 606 4 HETNAM CP PHOSPHORIC ACID MONO(FORMAMIDE)ESTER HETNAM APC DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER HETNAM MN MANGANESE (II) ION HETNAM K POTASSIUM ION HETNAM FE2 FE (II) ION HETNAM EDO 1,2-ETHANEDIOL HETSYN APC ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE HETSYN EDO ETHYLENE GLYCOL FORMUL 2 CP C H4 N O5 P FORMUL 3 APC C11 H18 N5 O12 P3 FORMUL 4 MN MN 2+ FORMUL 5 K K 1+ FORMUL 6 FE2 FE 2+ FORMUL 7 EDO C2 H6 O2 FORMUL 8 HOH *260(H2 O) HELIX 1 1 GLU A 32 ARG A 37 1 6 HELIX 2 2 LYS A 38 TYR A 42 5 5 HELIX 3 3 PRO A 46 GLY A 58 1 13 HELIX 4 4 THR A 60 LEU A 64 5 5 HELIX 5 5 ASP A 72 LEU A 81 1 10 HELIX 6 6 SER A 87 LEU A 96 1 10 HELIX 7 7 GLN A 113 TYR A 124 1 12 HELIX 8 8 SER A 166 THR A 178 1 13 HELIX 9 9 ASN A 184 ALA A 192 1 9 HELIX 10 10 ALA A 193 GLY A 195 5 3 HELIX 11 11 GLU A 229 TYR A 245 1 17 HELIX 12 12 ASP A 270 GLU A 273 5 4 HELIX 13 13 TYR A 274 GLY A 301 1 28 HELIX 14 14 GLY A 309 LEU A 313 5 5 HELIX 15 15 ASN A 314 THR A 323 1 10 HELIX 16 16 SER A 337 ILE A 339 5 3 HELIX 17 17 GLY A 340 LEU A 353 1 14 HELIX 18 18 SER A 371 GLY A 383 1 13 HELIX 19 19 ASN A 391 SER A 402 1 12 HELIX 20 20 THR A 433 ARG A 441 1 9 HELIX 21 21 VAL A 459 LEU A 464 1 6 HELIX 22 22 ARG A 480 GLU A 485 1 6 HELIX 23 23 LEU A 487 VAL A 491 5 5 HELIX 24 24 ASN A 507 GLY A 522 1 16 HELIX 25 25 SER A 541 LEU A 552 1 12 SHEET 1 A 5 ARG A 25 GLU A 31 0 SHEET 2 A 5 SER A 17 VAL A 22 -1 N LEU A 20 O ALA A 28 SHEET 3 A 5 ARG A 2 ASN A 7 -1 N GLY A 5 O ALA A 19 SHEET 4 A 5 ALA A 66 PHE A 69 1 O ALA A 68 N LEU A 6 SHEET 5 A 5 LEU A 109 PHE A 111 1 O HIS A 110 N PHE A 69 SHEET 1 B 5 LYS A 154 PRO A 162 0 SHEET 2 B 5 GLU A 143 GLU A 151 -1 N LEU A 147 O LEU A 158 SHEET 3 B 5 GLY A 131 VAL A 136 -1 N VAL A 133 O ALA A 148 SHEET 4 B 5 THR A 304 ALA A 308 1 O PHE A 306 N ALA A 132 SHEET 5 B 5 LYS A 329 PHE A 331 1 O PHE A 331 N LEU A 305 SHEET 1 C 2 PHE A 205 ASP A 208 0 SHEET 2 C 2 GLY A 211 LEU A 214 -1 O ARG A 213 N ALA A 206 SHEET 1 D 2 PHE A 252 TYR A 256 0 SHEET 2 D 2 VAL A 263 THR A 267 -1 O ASP A 266 N VAL A 253 SHEET 1 E 7 GLN A 500 VAL A 502 0 SHEET 2 E 7 PRO A 453 LEU A 456 1 N MET A 455 O VAL A 502 SHEET 3 E 7 VAL A 525 SER A 530 -1 O CYS A 526 N SER A 454 SHEET 4 E 7 ARG A 423 SER A 428 -1 N LEU A 425 O THR A 529 SHEET 5 E 7 VAL A 406 ALA A 409 -1 N TRP A 408 O SER A 424 SHEET 6 E 7 ALA A 556 VAL A 559 1 O ALA A 558 N GLY A 407 SHEET 7 E 7 TYR A 562 THR A 565 -1 O VAL A 564 N LEU A 557 SHEET 1 F 2 THR A 477 LYS A 478 0 SHEET 2 F 2 SER A 496 THR A 497 -1 O THR A 497 N THR A 477 LINK NE2 HIS A 114 FE FE2 A 605 1555 1555 2.35 LINK NE2 HIS A 118 FE FE2 A 605 1555 1555 2.31 LINK OD2 ASP A 137 FE FE2 A 605 1555 1555 2.39 LINK OD1 ASP A 137 FE FE2 A 605 1555 1555 2.43 LINK OD2 ASP A 338 FE FE2 A 605 1555 1555 2.19 LINK OG SER A 530 MN MN A 603 1555 1555 2.28 LINK O2P CP A 601 MN MN A 603 1555 1555 2.37 LINK O2G APC A 602 MN MN A 603 1555 1555 2.45 LINK O2B APC A 602 MN MN A 603 1555 1555 2.64 LINK MN MN A 603 O HOH A 701 1555 1555 2.49 LINK MN MN A 603 O HOH A 702 1555 1555 2.42 LINK FE FE2 A 605 O HOH A 815 1555 1555 2.44 SITE 1 AC1 13 ARG A 418 ALA A 419 LYS A 443 MET A 473 SITE 2 AC1 13 ARG A 498 ASN A 528 THR A 529 SER A 530 SITE 3 AC1 13 APC A 602 MN A 603 HOH A 702 HOH A 703 SITE 4 AC1 13 HOH A 816 SITE 1 AC2 25 GLY A 186 LYS A 187 MET A 189 THR A 316 SITE 2 AC2 25 ARG A 418 LYS A 443 ARG A 445 ARG A 449 SITE 3 AC2 25 PRO A 450 HIS A 492 SER A 496 THR A 497 SITE 4 AC2 25 ARG A 498 SER A 530 ASN A 532 ARG A 534 SITE 5 AC2 25 GLY A 535 CP A 601 MN A 603 HOH A 701 SITE 6 AC2 25 HOH A 729 HOH A 804 HOH A 824 HOH A 827 SITE 7 AC2 25 HOH A 835 SITE 1 AC3 5 SER A 530 CP A 601 APC A 602 HOH A 701 SITE 2 AC3 5 HOH A 702 SITE 1 AC4 5 HIS A 114 HIS A 118 ASP A 137 ASP A 338 SITE 2 AC4 5 HOH A 815 SITE 1 AC5 7 GLU A 369 PHE A 370 ALA A 409 GLN A 410 SITE 2 AC5 7 GLY A 411 GLY A 560 HOH A 813 CRYST1 98.741 98.741 281.099 90.00 90.00 120.00 P 61 2 2 12 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 0.010128 0.005847 0.000000 0.00000 SCALE2 0.000000 0.011694 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003557 0.00000