HEADER TRANSFERASE 09-JAN-12 3VF4 TITLE CRYSTAL STRUCTURE OF THE O-CARBAMOYLTRANSFERASE TOBZ S530A VARIANT IN TITLE 2 COMPLEX WITH CARBAMOYL PHOSPHATE AND ADP 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 4 13-SEP-23 3VF4 1 REMARK SEQADV LINK REVDAT 3 02-MAY-12 3VF4 1 JRNL REVDAT 2 14-MAR-12 3VF4 1 JRNL REVDAT 1 25-JAN-12 3VF4 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. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.7.1_743 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.30 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 32754 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.174 REMARK 3 R VALUE (WORKING SET) : 0.171 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1639 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 29.3067 - 5.4837 0.98 2804 150 0.1722 0.2005 REMARK 3 2 5.4837 - 4.3571 1.00 2696 141 0.1335 0.1689 REMARK 3 3 4.3571 - 3.8077 1.00 2624 139 0.1348 0.1842 REMARK 3 4 3.8077 - 3.4602 1.00 2609 138 0.1606 0.2236 REMARK 3 5 3.4602 - 3.2125 1.00 2599 136 0.1758 0.2206 REMARK 3 6 3.2125 - 3.0233 1.00 2567 135 0.1771 0.2529 REMARK 3 7 3.0233 - 2.8720 1.00 2583 136 0.1842 0.2707 REMARK 3 8 2.8720 - 2.7471 1.00 2536 135 0.1989 0.2468 REMARK 3 9 2.7471 - 2.6414 1.00 2559 134 0.2090 0.3050 REMARK 3 10 2.6414 - 2.5503 1.00 2519 133 0.2066 0.3060 REMARK 3 11 2.5503 - 2.4706 0.99 2540 132 0.2044 0.2650 REMARK 3 12 2.4706 - 2.4000 0.98 2479 130 0.2142 0.2933 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 : 0.95 REMARK 3 K_SOL : 0.36 REMARK 3 B_SOL : 22.34 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.620 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.340 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.58 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.16 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.88760 REMARK 3 B22 (A**2) : 1.88760 REMARK 3 B33 (A**2) : -3.77520 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 : 0.007 4533 REMARK 3 ANGLE : 1.088 6184 REMARK 3 CHIRALITY : 0.069 670 REMARK 3 PLANARITY : 0.005 818 REMARK 3 DIHEDRAL : 13.550 1640 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 3VF4 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_1000069966. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-AUG-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32764 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 29.476 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 5.800 REMARK 200 R MERGE (I) : 0.11900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.9900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.50 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.2 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.45100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.170 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 (%): 60.86 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.14 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 93.48133 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 186.96267 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 140.22200 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 233.70333 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 46.74067 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 93.48133 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 186.96267 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 233.70333 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 140.22200 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 46.74067 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 891 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 HIS A 0 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: 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 OE2 GLU A 172 O3' ADP A 603 2.16 REMARK 500 O HOH A 992 O HOH A 1017 2.16 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 40 -4.78 83.87 REMARK 500 ALA A 122 -63.43 -99.49 REMARK 500 ASP A 137 -156.24 -136.31 REMARK 500 GLU A 142 -63.37 -126.72 REMARK 500 GLU A 142 -51.65 -136.92 REMARK 500 ALA A 204 -45.47 -135.37 REMARK 500 VAL A 335 46.69 -101.79 REMARK 500 ARG A 445 -154.93 -129.14 REMARK 500 ALA A 484 3.61 -69.40 REMARK 500 LEU A 487 57.12 -118.47 REMARK 500 ASN A 507 78.97 -167.92 REMARK 500 SER A 540 -55.67 -121.73 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 601 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 114 NE2 REMARK 620 2 HIS A 118 NE2 90.0 REMARK 620 3 ASP A 137 OD1 101.6 99.5 REMARK 620 4 ASP A 338 OD2 92.0 91.5 162.4 REMARK 620 5 ADP A 603 O3B 85.2 174.9 83.0 87.2 REMARK 620 6 ADP A 603 O1A 161.5 96.5 94.4 70.6 87.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 602 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LEU A 322 O REMARK 620 2 ARG A 324 O 80.0 REMARK 620 3 VAL A 327 O 84.6 65.0 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 FE2 A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP A 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CP A 604 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: 3VES RELATED DB: PDB REMARK 900 TOBZ IN COMPLEX WITH AMPCPP AND CARBAMOYL PHOSPHATE 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 DBREF 3VF4 A 1 570 UNP Q70IY1 Q70IY1_STRSD 1 570 SEQADV 3VF4 HIS A -5 UNP Q70IY1 EXPRESSION TAG SEQADV 3VF4 HIS A -4 UNP Q70IY1 EXPRESSION TAG SEQADV 3VF4 HIS A -3 UNP Q70IY1 EXPRESSION TAG SEQADV 3VF4 HIS A -2 UNP Q70IY1 EXPRESSION TAG SEQADV 3VF4 HIS A -1 UNP Q70IY1 EXPRESSION TAG SEQADV 3VF4 HIS A 0 UNP Q70IY1 EXPRESSION TAG SEQADV 3VF4 ALA A 530 UNP Q70IY1 SER 530 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 PHE 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 ALA 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 FE2 A 601 1 HET K A 602 1 HET ADP A 603 27 HET CP A 604 8 HETNAM FE2 FE (II) ION HETNAM K POTASSIUM ION HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM CP PHOSPHORIC ACID MONO(FORMAMIDE)ESTER FORMUL 2 FE2 FE 2+ FORMUL 3 K K 1+ FORMUL 4 ADP C10 H15 N5 O10 P2 FORMUL 5 CP C H4 N O5 P FORMUL 6 HOH *390(H2 O) HELIX 1 1 GLU A 32 ARG A 37 1 6 HELIX 2 2 PRO A 46 GLY A 58 1 13 HELIX 3 3 THR A 60 LEU A 64 5 5 HELIX 4 4 ASP A 72 LEU A 81 1 10 HELIX 5 5 SER A 87 LEU A 96 1 10 HELIX 6 6 GLN A 113 TYR A 124 1 12 HELIX 7 7 SER A 166 THR A 178 1 13 HELIX 8 8 ASN A 184 ALA A 193 1 10 HELIX 9 9 GLU A 229 TYR A 245 1 17 HELIX 10 10 ASP A 270 GLU A 273 5 4 HELIX 11 11 TYR A 274 GLY A 301 1 28 HELIX 12 12 GLY A 309 LEU A 313 5 5 HELIX 13 13 ASN A 314 THR A 323 1 10 HELIX 14 14 SER A 337 ILE A 339 5 3 HELIX 15 15 GLY A 340 LEU A 353 1 14 HELIX 16 16 SER A 371 GLY A 383 1 13 HELIX 17 17 ASN A 391 SER A 402 1 12 HELIX 18 18 THR A 433 ARG A 441 1 9 HELIX 19 19 ARG A 457 LEU A 464 1 8 HELIX 20 20 ASN A 507 GLY A 522 1 16 HELIX 21 21 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 THR A 304 N ALA A 132 SHEET 5 B 5 LYS A 329 PHE A 331 1 O LYS A 329 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 GLY A 211 N ASP A 208 SHEET 1 D 2 PHE A 252 ASP A 257 0 SHEET 2 D 2 ARG A 262 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 GLN A 500 SHEET 3 E 7 VAL A 525 ALA A 530 -1 O CYS A 526 N SER A 454 SHEET 4 E 7 ARG A 423 SER A 428 -1 N GLY A 427 O LEU A 527 SHEET 5 E 7 VAL A 406 ALA A 409 -1 N VAL A 406 O LEU A 426 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 601 1555 1555 2.16 LINK NE2 HIS A 118 FE FE2 A 601 1555 1555 2.18 LINK OD1 ASP A 137 FE FE2 A 601 1555 1555 2.05 LINK O LEU A 322 K K A 602 1555 1555 3.16 LINK O ARG A 324 K K A 602 1555 1555 3.12 LINK O VAL A 327 K K A 602 1555 1555 2.97 LINK OD2 ASP A 338 FE FE2 A 601 1555 1555 2.12 LINK FE FE2 A 601 O3B ADP A 603 1555 1555 2.24 LINK FE FE2 A 601 O1A ADP A 603 1555 1555 2.28 SITE 1 AC1 5 HIS A 114 HIS A 118 ASP A 137 ASP A 338 SITE 2 AC1 5 ADP A 603 SITE 1 AC2 3 LEU A 322 ARG A 324 VAL A 327 SITE 1 AC3 18 HIS A 14 HIS A 114 HIS A 118 ASP A 137 SITE 2 AC3 18 GLY A 138 GLN A 139 GLY A 168 TYR A 171 SITE 3 AC3 18 GLU A 172 PRO A 185 GLY A 310 VAL A 311 SITE 4 AC3 18 LEU A 313 ASN A 314 SER A 337 ASP A 338 SITE 5 AC3 18 FE2 A 601 HOH A 814 SITE 1 AC4 11 ARG A 418 ALA A 419 MET A 473 ARG A 498 SITE 2 AC4 11 ASN A 528 THR A 529 ALA A 530 HOH A 702 SITE 3 AC4 11 HOH A 712 HOH A 742 HOH A 745 CRYST1 99.247 99.247 280.444 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 0.010076 0.005817 0.000000 0.00000 SCALE2 0.000000 0.011635 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003566 0.00000