HEADER TRANSFERASE 11-DEC-07 2VJO TITLE FORMYL-COA TRANSFERASE MUTANT VARIANT Q17A WITH ASPARTYL-COA THIOESTER TITLE 2 INTERMEDIATES AND OXALATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: FORMYL-COENZYME A TRANSFERASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: FORMYL-COA TRANSFERASE; COMPND 5 EC: 2.8.3.16; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: OXALOBACTER FORMIGENES; SOURCE 3 ORGANISM_TAXID: 847; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PET-9A KEYWDS CYTOPLASM, TRANSFERASE, CLASS III COA TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR C.L.BERTHOLD,C.G.TOYOTA,N.G.J.RICHARDS,Y.LINDQVIST REVDAT 5 13-DEC-23 2VJO 1 LINK REVDAT 4 17-JAN-18 2VJO 1 REMARK REVDAT 3 24-FEB-09 2VJO 1 VERSN REVDAT 2 11-MAR-08 2VJO 1 JRNL REVDAT 1 25-DEC-07 2VJO 0 JRNL AUTH C.L.BERTHOLD,C.G.TOYOTA,N.G.J.RICHARDS,Y.LINDQVIST JRNL TITL REINVESTIGATION OF THE CATALYTIC MECHANISM OF FORMYL-COA JRNL TITL 2 TRANSFERASE, A CLASS III COA-TRANSFERASE. JRNL REF J.BIOL.CHEM. V. 283 6519 2008 JRNL REFN ISSN 0021-9258 JRNL PMID 18162462 JRNL DOI 10.1074/JBC.M709353200 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 54545 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.208 REMARK 3 R VALUE (WORKING SET) : 0.206 REMARK 3 FREE R VALUE : 0.248 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2894 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4026 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2850 REMARK 3 BIN FREE R VALUE SET COUNT : 201 REMARK 3 BIN FREE R VALUE : 0.3240 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6616 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 119 REMARK 3 SOLVENT ATOMS : 440 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.86 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.21000 REMARK 3 B22 (A**2) : 0.21000 REMARK 3 B33 (A**2) : -0.42000 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 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.245 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.202 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.148 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.752 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.936 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.903 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6929 ; 0.010 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9403 ; 1.153 ; 1.975 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 866 ; 5.735 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 314 ;38.340 ;24.936 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1163 ;15.102 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 34 ;18.826 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1003 ; 0.095 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5284 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 3286 ; 0.175 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 4660 ; 0.295 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 462 ; 0.140 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 21 ; 0.169 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 7 ; 0.146 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 4407 ; 0.531 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6826 ; 0.926 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2913 ; 1.007 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2570 ; 1.557 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. REMARK 4 REMARK 4 2VJO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 11-DEC-07. REMARK 100 THE DEPOSITION ID IS D_1290034519. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-OCT-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : MAX II REMARK 200 BEAMLINE : I911-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.037 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 57462 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 41.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : 0.12000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.32 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.57000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 1P5H REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.86 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 4 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -Y,X,Z REMARK 290 4555 Y,-X,Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -Y+1/2,X+1/2,Z+1/2 REMARK 290 8555 Y+1/2,-X+1/2,Z+1/2 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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 76.79650 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 76.79650 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 49.02750 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 76.79650 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 76.79650 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 49.02750 REMARK 290 SMTRY1 7 0.000000 -1.000000 0.000000 76.79650 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 76.79650 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 49.02750 REMARK 290 SMTRY1 8 0.000000 1.000000 0.000000 76.79650 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 76.79650 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 49.02750 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 TOTAL BURIED SURFACE AREA: 14140 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 36300 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -94.4 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED RESIDUE IN CHAIN A, GLN 17 TO ALA REMARK 400 ENGINEERED RESIDUE IN CHAIN B, GLN 17 TO ALA 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 MET A 1 REMARK 465 MET B 1 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 2105 O HOH A 2107 2.12 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 VAL A 16 -125.76 68.57 REMARK 500 ASN A 64 23.68 -142.14 REMARK 500 LYS A 75 30.54 -88.09 REMARK 500 ASN A 96 47.13 -140.22 REMARK 500 PHE A 107 63.39 -101.73 REMARK 500 ASP A 169 -73.13 -78.13 REMARK 500 LYS A 316 10.35 -144.44 REMARK 500 VAL B 16 -123.13 66.46 REMARK 500 LYS B 75 34.47 -95.58 REMARK 500 ASP B 169 -82.19 -85.60 REMARK 500 LYS B 189 -69.84 -92.09 REMARK 500 ASP B 237 -157.60 -97.89 REMARK 500 LYS B 316 28.90 -147.14 REMARK 500 PRO B 346 63.23 -67.54 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE COA A1169 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A1429 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE COA B1169 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B1429 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE OXL A1430 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EPE A1431 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1P5H RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF FORMYL-COA TRANSFERASE ( APOENZYME)FROM REMARK 900 OXALOBACTER FORMIGENES REMARK 900 RELATED ID: 1P5R RELATED DB: PDB REMARK 900 FORMYL-COA TRANSFERASE IN COMPLEX WITH COENZYME A REMARK 900 RELATED ID: 1T3Z RELATED DB: PDB REMARK 900 FORMYL-COA TRANFERASE MUTANT ASP169 TO SER REMARK 900 RELATED ID: 1T4C RELATED DB: PDB REMARK 900 FORMYL-COA TRANSFERASE IN COMPLEX WITH OXALYL-COA REMARK 900 RELATED ID: 1VGR RELATED DB: PDB REMARK 900 FORMYL-COA TRANSFERASE MUTANT ASP169 TO GLU REMARK 900 RELATED ID: 1VGQ RELATED DB: PDB REMARK 900 FORMYL-COA TRANSFERASE MUTANT ASP169 TO ALA REMARK 900 RELATED ID: 2VJQ RELATED DB: PDB REMARK 900 FORMYL-COA TRANSFERASE MUTANT VARIANT W48Q REMARK 900 RELATED ID: 2VJK RELATED DB: PDB REMARK 900 FORMYL-COA TRANSFERASE WITH ASPARTYL-COA THIOESTER INTERMEDIATE REMARK 900 DERIVED FROM OXALYL-COA REMARK 900 RELATED ID: 2VJM RELATED DB: PDB REMARK 900 FORMYL-COA TRANSFERASE WITH ASPARTYL-FORMYL ANHYDIDE INTERMEDIATE REMARK 900 RELATED ID: 2VJN RELATED DB: PDB REMARK 900 FORMYL-COA TRANSFERASE MUTANT VARIANT G260A REMARK 900 RELATED ID: 2VJP RELATED DB: PDB REMARK 900 FORMYL-COA TRANSFERASE MUTANT VARIANT W48F REMARK 900 RELATED ID: 2VJL RELATED DB: PDB REMARK 900 FORMYL-COA TRANSFERASE WITH ASPARTYL-COA THIOESTER INTERMEDIATE REMARK 900 DERIVED FROM FORMYL-COA REMARK 999 REMARK 999 SEQUENCE REMARK 999 ACCORDING TO THE DEPOSITORS OF THIS ENTRY, THE SEQADV REMARK 999 LISTED BELOW IS DUE TO AN ERROR IN THE UNIPROT ENTRY REMARK 999 O06644. THE IDENTITY OF RESIDUE 186 HAS BEEN CONFIRMED REMARK 999 AS ILE. DBREF 2VJO A 1 428 UNP O06644 FCTA_OXAFO 1 428 DBREF 2VJO B 1 428 UNP O06644 FCTA_OXAFO 1 428 SEQADV 2VJO ALA A 17 UNP O06644 GLN 17 ENGINEERED MUTATION SEQADV 2VJO ALA B 17 UNP O06644 GLN 17 ENGINEERED MUTATION SEQADV 2VJO ILE A 186 UNP O06644 MET 186 CONFLICT SEQADV 2VJO ILE B 186 UNP O06644 MET 186 CONFLICT SEQRES 1 A 428 MET THR LYS PRO LEU ASP GLY ILE ASN VAL LEU ASP PHE SEQRES 2 A 428 THR HIS VAL ALA ALA GLY PRO ALA CYS THR GLN MET MET SEQRES 3 A 428 GLY PHE LEU GLY ALA ASN VAL ILE LYS ILE GLU ARG ARG SEQRES 4 A 428 GLY SER GLY ASP MET THR ARG GLY TRP LEU GLN ASP LYS SEQRES 5 A 428 PRO ASN VAL ASP SER LEU TYR PHE THR MET PHE ASN CYS SEQRES 6 A 428 ASN LYS ARG SER ILE GLU LEU ASP MET LYS THR PRO GLU SEQRES 7 A 428 GLY LYS GLU LEU LEU GLU GLN MET ILE LYS LYS ALA ASP SEQRES 8 A 428 VAL MET VAL GLU ASN PHE GLY PRO GLY ALA LEU ASP ARG SEQRES 9 A 428 MET GLY PHE THR TRP GLU TYR ILE GLN GLU LEU ASN PRO SEQRES 10 A 428 ARG VAL ILE LEU ALA SER VAL LYS GLY TYR ALA GLU GLY SEQRES 11 A 428 HIS ALA ASN GLU HIS LEU LYS VAL TYR GLU ASN VAL ALA SEQRES 12 A 428 GLN CYS SER GLY GLY ALA ALA ALA THR THR GLY PHE TRP SEQRES 13 A 428 ASP GLY PRO PRO THR VAL SER GLY ALA ALA LEU GLY ASP SEQRES 14 A 428 SER ASN SER GLY MET HIS LEU MET ILE GLY ILE LEU ALA SEQRES 15 A 428 ALA LEU GLU ILE ARG HIS LYS THR GLY ARG GLY GLN LYS SEQRES 16 A 428 VAL ALA VAL ALA MET GLN ASP ALA VAL LEU ASN LEU VAL SEQRES 17 A 428 ARG ILE LYS LEU ARG ASP GLN GLN ARG LEU GLU ARG THR SEQRES 18 A 428 GLY ILE LEU ALA GLU TYR PRO GLN ALA GLN PRO ASN PHE SEQRES 19 A 428 ALA PHE ASP ARG ASP GLY ASN PRO LEU SER PHE ASP ASN SEQRES 20 A 428 ILE THR SER VAL PRO ARG GLY GLY ASN ALA GLY GLY GLY SEQRES 21 A 428 GLY GLN PRO GLY TRP MET LEU LYS CYS LYS GLY TRP GLU SEQRES 22 A 428 THR ASP ALA ASP SER TYR VAL TYR PHE THR ILE ALA ALA SEQRES 23 A 428 ASN MET TRP PRO GLN ILE CYS ASP MET ILE ASP LYS PRO SEQRES 24 A 428 GLU TRP LYS ASP ASP PRO ALA TYR ASN THR PHE GLU GLY SEQRES 25 A 428 ARG VAL ASP LYS LEU MET ASP ILE PHE SER PHE ILE GLU SEQRES 26 A 428 THR LYS PHE ALA ASP LYS ASP LYS PHE GLU VAL THR GLU SEQRES 27 A 428 TRP ALA ALA GLN TYR GLY ILE PRO CYS GLY PRO VAL MET SEQRES 28 A 428 SER MET LYS GLU LEU ALA HIS ASP PRO SER LEU GLN LYS SEQRES 29 A 428 VAL GLY THR VAL VAL GLU VAL VAL ASP GLU ILE ARG GLY SEQRES 30 A 428 ASN HIS LEU THR VAL GLY ALA PRO PHE LYS PHE SER GLY SEQRES 31 A 428 PHE GLN PRO GLU ILE THR ARG ALA PRO LEU LEU GLY GLU SEQRES 32 A 428 HIS THR ASP GLU VAL LEU LYS GLU LEU GLY LEU ASP ASP SEQRES 33 A 428 ALA LYS ILE LYS GLU LEU HIS ALA LYS GLN VAL VAL SEQRES 1 B 428 MET THR LYS PRO LEU ASP GLY ILE ASN VAL LEU ASP PHE SEQRES 2 B 428 THR HIS VAL ALA ALA GLY PRO ALA CYS THR GLN MET MET SEQRES 3 B 428 GLY PHE LEU GLY ALA ASN VAL ILE LYS ILE GLU ARG ARG SEQRES 4 B 428 GLY SER GLY ASP MET THR ARG GLY TRP LEU GLN ASP LYS SEQRES 5 B 428 PRO ASN VAL ASP SER LEU TYR PHE THR MET PHE ASN CYS SEQRES 6 B 428 ASN LYS ARG SER ILE GLU LEU ASP MET LYS THR PRO GLU SEQRES 7 B 428 GLY LYS GLU LEU LEU GLU GLN MET ILE LYS LYS ALA ASP SEQRES 8 B 428 VAL MET VAL GLU ASN PHE GLY PRO GLY ALA LEU ASP ARG SEQRES 9 B 428 MET GLY PHE THR TRP GLU TYR ILE GLN GLU LEU ASN PRO SEQRES 10 B 428 ARG VAL ILE LEU ALA SER VAL LYS GLY TYR ALA GLU GLY SEQRES 11 B 428 HIS ALA ASN GLU HIS LEU LYS VAL TYR GLU ASN VAL ALA SEQRES 12 B 428 GLN CYS SER GLY GLY ALA ALA ALA THR THR GLY PHE TRP SEQRES 13 B 428 ASP GLY PRO PRO THR VAL SER GLY ALA ALA LEU GLY ASP SEQRES 14 B 428 SER ASN SER GLY MET HIS LEU MET ILE GLY ILE LEU ALA SEQRES 15 B 428 ALA LEU GLU ILE ARG HIS LYS THR GLY ARG GLY GLN LYS SEQRES 16 B 428 VAL ALA VAL ALA MET GLN ASP ALA VAL LEU ASN LEU VAL SEQRES 17 B 428 ARG ILE LYS LEU ARG ASP GLN GLN ARG LEU GLU ARG THR SEQRES 18 B 428 GLY ILE LEU ALA GLU TYR PRO GLN ALA GLN PRO ASN PHE SEQRES 19 B 428 ALA PHE ASP ARG ASP GLY ASN PRO LEU SER PHE ASP ASN SEQRES 20 B 428 ILE THR SER VAL PRO ARG GLY GLY ASN ALA GLY GLY GLY SEQRES 21 B 428 GLY GLN PRO GLY TRP MET LEU LYS CYS LYS GLY TRP GLU SEQRES 22 B 428 THR ASP ALA ASP SER TYR VAL TYR PHE THR ILE ALA ALA SEQRES 23 B 428 ASN MET TRP PRO GLN ILE CYS ASP MET ILE ASP LYS PRO SEQRES 24 B 428 GLU TRP LYS ASP ASP PRO ALA TYR ASN THR PHE GLU GLY SEQRES 25 B 428 ARG VAL ASP LYS LEU MET ASP ILE PHE SER PHE ILE GLU SEQRES 26 B 428 THR LYS PHE ALA ASP LYS ASP LYS PHE GLU VAL THR GLU SEQRES 27 B 428 TRP ALA ALA GLN TYR GLY ILE PRO CYS GLY PRO VAL MET SEQRES 28 B 428 SER MET LYS GLU LEU ALA HIS ASP PRO SER LEU GLN LYS SEQRES 29 B 428 VAL GLY THR VAL VAL GLU VAL VAL ASP GLU ILE ARG GLY SEQRES 30 B 428 ASN HIS LEU THR VAL GLY ALA PRO PHE LYS PHE SER GLY SEQRES 31 B 428 PHE GLN PRO GLU ILE THR ARG ALA PRO LEU LEU GLY GLU SEQRES 32 B 428 HIS THR ASP GLU VAL LEU LYS GLU LEU GLY LEU ASP ASP SEQRES 33 B 428 ALA LYS ILE LYS GLU LEU HIS ALA LYS GLN VAL VAL HET COA A1169 48 HET CL A1429 1 HET OXL A1430 6 HET EPE A1431 15 HET COA B1169 48 HET CL B1429 1 HETNAM COA COENZYME A HETNAM CL CHLORIDE ION HETNAM OXL OXALATE ION HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HETSYN EPE HEPES FORMUL 3 COA 2(C21 H36 N7 O16 P3 S) FORMUL 4 CL 2(CL 1-) FORMUL 5 OXL C2 O4 2- FORMUL 6 EPE C8 H18 N2 O4 S FORMUL 9 HOH *440(H2 O) HELIX 1 1 ALA A 17 LEU A 29 1 13 HELIX 2 2 ASP A 43 GLY A 47 5 5 HELIX 3 3 SER A 57 MET A 62 1 6 HELIX 4 4 THR A 76 LYS A 89 1 14 HELIX 5 5 LEU A 102 GLY A 106 5 5 HELIX 6 6 THR A 108 ASN A 116 1 9 HELIX 7 7 TYR A 139 GLY A 147 1 9 HELIX 8 8 ALA A 149 THR A 153 5 5 HELIX 9 9 GLY A 168 GLY A 191 1 24 HELIX 10 10 MET A 200 VAL A 208 1 9 HELIX 11 11 VAL A 208 GLY A 222 1 15 HELIX 12 12 TYR A 227 GLN A 231 5 5 HELIX 13 13 ALA A 285 ASN A 287 5 3 HELIX 14 14 MET A 288 ILE A 296 1 9 HELIX 15 15 LYS A 298 LYS A 302 5 5 HELIX 16 16 THR A 309 VAL A 314 1 6 HELIX 17 17 LYS A 316 LYS A 327 1 12 HELIX 18 18 ASP A 332 GLN A 342 1 11 HELIX 19 19 SER A 352 HIS A 358 1 7 HELIX 20 20 ASP A 359 VAL A 365 1 7 HELIX 21 21 HIS A 404 LEU A 412 1 9 HELIX 22 22 ASP A 415 LYS A 425 1 11 HELIX 23 23 ALA B 17 LEU B 29 1 13 HELIX 24 24 ASP B 43 TRP B 48 5 6 HELIX 25 25 SER B 57 MET B 62 1 6 HELIX 26 26 THR B 76 ALA B 90 1 15 HELIX 27 27 GLY B 100 MET B 105 1 6 HELIX 28 28 THR B 108 ASN B 116 1 9 HELIX 29 29 TYR B 139 GLY B 147 1 9 HELIX 30 30 ALA B 149 THR B 153 5 5 HELIX 31 31 GLY B 168 GLY B 191 1 24 HELIX 32 32 MET B 200 VAL B 208 1 9 HELIX 33 33 VAL B 208 GLY B 222 1 15 HELIX 34 34 TYR B 227 GLN B 231 5 5 HELIX 35 35 MET B 288 ILE B 296 1 9 HELIX 36 36 LYS B 298 ASP B 303 5 6 HELIX 37 37 THR B 309 VAL B 314 1 6 HELIX 38 38 LYS B 316 PHE B 328 1 13 HELIX 39 39 ALA B 329 LYS B 331 5 3 HELIX 40 40 ASP B 332 GLN B 342 1 11 HELIX 41 41 SER B 352 HIS B 358 1 7 HELIX 42 42 ASP B 359 VAL B 365 1 7 HELIX 43 43 HIS B 404 LEU B 412 1 9 HELIX 44 44 ASP B 415 LYS B 425 1 11 SHEET 1 AA 7 ARG A 68 GLU A 71 0 SHEET 2 AA 7 ASN A 32 GLU A 37 1 O VAL A 33 N ARG A 68 SHEET 3 AA 7 ASN A 9 ASP A 12 1 O VAL A 10 N ILE A 34 SHEET 4 AA 7 VAL A 92 GLU A 95 1 O VAL A 92 N LEU A 11 SHEET 5 AA 7 ILE A 120 LYS A 125 1 O ILE A 120 N MET A 93 SHEET 6 AA 7 LYS A 195 ALA A 199 1 O VAL A 196 N SER A 123 SHEET 7 AA 7 PHE B 386 PHE B 388 -1 O LYS B 387 N ALA A 197 SHEET 1 AB 3 GLY A 264 LYS A 268 0 SHEET 2 AB 3 TYR A 279 THR A 283 -1 O VAL A 280 N LEU A 267 SHEET 3 AB 3 CYS A 347 PRO A 349 -1 O GLY A 348 N TYR A 281 SHEET 1 AC 2 VAL A 368 VAL A 371 0 SHEET 2 AC 2 HIS A 379 VAL A 382 -1 O HIS A 379 N VAL A 371 SHEET 1 AD 7 PHE A 386 PHE A 388 0 SHEET 2 AD 7 LYS B 195 ALA B 199 -1 O ALA B 197 N LYS A 387 SHEET 3 AD 7 ILE B 120 LYS B 125 1 O LEU B 121 N VAL B 196 SHEET 4 AD 7 VAL B 92 GLU B 95 1 O MET B 93 N ALA B 122 SHEET 5 AD 7 ASN B 9 ASP B 12 1 O LEU B 11 N VAL B 94 SHEET 6 AD 7 ASN B 32 GLU B 37 1 O ASN B 32 N VAL B 10 SHEET 7 AD 7 ARG B 68 GLU B 71 1 O ARG B 68 N LYS B 35 SHEET 1 BA 3 GLY B 264 LYS B 268 0 SHEET 2 BA 3 TYR B 279 THR B 283 -1 O VAL B 280 N LEU B 267 SHEET 3 BA 3 CYS B 347 PRO B 349 -1 O GLY B 348 N TYR B 281 SHEET 1 BB 2 VAL B 368 VAL B 371 0 SHEET 2 BB 2 HIS B 379 VAL B 382 -1 O HIS B 379 N VAL B 371 LINK CG ASP A 169 S1P COA A1169 1555 1555 1.79 LINK CG ASP B 169 S1P COA B1169 1555 1555 1.44 SITE 1 AC1 23 HIS A 15 ALA A 18 ARG A 38 MET A 44 SITE 2 AC1 23 LEU A 72 ASP A 73 MET A 74 LYS A 75 SITE 3 AC1 23 ASN A 96 PHE A 97 GLY A 98 ARG A 104 SITE 4 AC1 23 MET A 105 VAL A 124 LYS A 137 VAL A 138 SITE 5 AC1 23 TYR A 139 ASP A 169 MET A 200 HOH A2078 SITE 6 AC1 23 HOH A2079 HOH A2080 HOH A2081 SITE 1 AC2 4 ALA A 17 PHE A 63 ALA A 166 SER A 170 SITE 1 AC3 20 LYS A 52 HIS B 15 ALA B 17 ALA B 18 SITE 2 AC3 20 ARG B 38 LEU B 72 ASP B 73 MET B 74 SITE 3 AC3 20 LYS B 75 ASN B 96 PHE B 97 GLY B 98 SITE 4 AC3 20 ARG B 104 MET B 105 LYS B 137 VAL B 138 SITE 5 AC3 20 ASP B 169 HOH B2049 HOH B2087 HOH B2088 SITE 1 AC4 5 PHE B 63 ALA B 166 ASP B 169 SER B 170 SITE 2 AC4 5 HOH B2073 SITE 1 AC5 8 GLY A 258 GLY A 260 GLY A 261 GLN A 262 SITE 2 AC5 8 HOH A2245 HOH A2246 GLU B 140 HOH B2037 SITE 1 AC6 11 TRP A 272 THR A 274 ASP A 275 ALA A 276 SITE 2 AC6 11 HOH A2144 HOH A2147 HOH A2148 HOH A2248 SITE 3 AC6 11 HOH A2249 ASP B 157 GLY B 158 CRYST1 153.593 153.593 98.055 90.00 90.00 90.00 I 4 16 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 0.006511 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006511 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010198 0.00000 MTRIX1 1 -0.865040 -0.494000 -0.087590 -59.71540 1 MTRIX2 1 -0.492000 0.801070 0.340920 -0.50925 1 MTRIX3 1 -0.098250 0.338000 -0.936000 -84.33185 1