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- PDB-2vjq: Formyl-CoA transferase mutant variant W48Q -

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Basic information

Entry
Database: PDB / ID: 2vjq
TitleFormyl-CoA transferase mutant variant W48Q
ComponentsFORMYL-COENZYME A TRANSFERASE
KeywordsTRANSFERASE / CLASS III COA TRANSFERASE
Function / homology
Function and homology information


formyl-CoA transferase / formyl-CoA transferase activity / oxalate catabolic process / cytoplasm
Similarity search - Function
Formyl-CoA:oxalate CoA-transferase / : / formyl-coa transferase, domain 3 / Crotonobetainyl-coa:carnitine coa-transferase; domain 1 / formyl-coa transferase, domain 3 / CoA-transferase family III / CoA-transferase family III domain 1 superfamily / CoA-transferase family III domain 3 superfamily / CoA-transferase family III / Rossmann fold ...Formyl-CoA:oxalate CoA-transferase / : / formyl-coa transferase, domain 3 / Crotonobetainyl-coa:carnitine coa-transferase; domain 1 / formyl-coa transferase, domain 3 / CoA-transferase family III / CoA-transferase family III domain 1 superfamily / CoA-transferase family III domain 3 superfamily / CoA-transferase family III / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Formyl-CoA:oxalate CoA-transferase
Similarity search - Component
Biological speciesOXALOBACTER FORMIGENES (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsToyota, C.G. / Berthold, C.L. / Gruez, A. / Jonsson, S. / Lindqvist, Y. / Cambillau, C. / Richards, N.G.J.
CitationJournal: J.Bacteriol. / Year: 2008
Title: Differential Substrate Specificity and Kinetic Behavior of Escherichia Coli Yfdw and Oxalobacter Formigenes Formyl Coenzyme a Transferase.
Authors: Toyota, C.G. / Berthold, C.L. / Gruez, A. / Jonsson, S. / Lindqvist, Y. / Cambillau, C. / Richards, N.G.J.
History
DepositionDec 11, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 15, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FORMYL-COENZYME A TRANSFERASE
B: FORMYL-COENZYME A TRANSFERASE
C: FORMYL-COENZYME A TRANSFERASE
D: FORMYL-COENZYME A TRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,6966
Polymers189,2194
Non-polymers4772
Water24,8431379
1
A: FORMYL-COENZYME A TRANSFERASE
B: FORMYL-COENZYME A TRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,8483
Polymers94,6102
Non-polymers2381
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12170 Å2
ΔGint-82.1 kcal/mol
Surface area30640 Å2
MethodPISA
2
C: FORMYL-COENZYME A TRANSFERASE
D: FORMYL-COENZYME A TRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,8483
Polymers94,6102
Non-polymers2381
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12160 Å2
ΔGint-84.3 kcal/mol
Surface area30870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)214.155, 98.917, 152.527
Angle α, β, γ (deg.)90.00, 135.27, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: 4 / Auth seq-ID: 2 - 428 / Label seq-ID: 2 - 428

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21CC
12BB
22DD

NCS ensembles :
ID
1
2

NCS oper: (Code: given
Matrix: (0.02134, 0.01307, -0.99969), (-0.00679, 0.99989, 0.01293), (0.99975, 0.00651, 0.02143)
Vector: 0.81646, -0.10161, -0.30258)

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Components

#1: Protein
FORMYL-COENZYME A TRANSFERASE / FORMYL-COA TRANSFERASE


Mass: 47304.781 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) OXALOBACTER FORMIGENES (bacteria) / Plasmid: PET-9A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O06644, formyl-CoA transferase
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1379 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, TRP 48 TO GLN ENGINEERED RESIDUE IN CHAIN B, TRP 48 TO GLN ...ENGINEERED RESIDUE IN CHAIN A, TRP 48 TO GLN ENGINEERED RESIDUE IN CHAIN B, TRP 48 TO GLN ENGINEERED RESIDUE IN CHAIN C, TRP 48 TO GLN ENGINEERED RESIDUE IN CHAIN D, TRP 48 TO GLN
Sequence detailsACCORDING TO THE DEPOSITORS OF THIS ENTRY, THE SEQADV LISTED BELOW IS DUE TO AN ERROR IN THE ...ACCORDING TO THE DEPOSITORS OF THIS ENTRY, THE SEQADV LISTED BELOW IS DUE TO AN ERROR IN THE UNIPROT ENTRY O06644. THE IDENTITY OF RESIDUE 186 HAS BEEN CONFIRMED AS ILE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.75 Å3/Da / Density % sol: 54.8 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 28, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.8→56.08 Å / Num. obs: 190053 / % possible obs: 92 % / Observed criterion σ(I): 2 / Redundancy: 2.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.4
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2.3 / % possible all: 68.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1P5H

1p5h


Resolution: 1.8→30 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.418 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.212 9536 5 %RANDOM
Rwork0.181 ---
obs0.182 180493 91.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.39 Å2
Baniso -1Baniso -2Baniso -3
1-0.94 Å20 Å20.63 Å2
2---1.09 Å20 Å2
3---1.06 Å2
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13232 0 30 1379 14641
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02213733
X-RAY DIFFRACTIONr_bond_other_d0.0010.029372
X-RAY DIFFRACTIONr_angle_refined_deg1.1131.95818619
X-RAY DIFFRACTIONr_angle_other_deg0.885322954
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.62851762
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.12825.039641
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.426152373
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7921569
X-RAY DIFFRACTIONr_chiral_restr0.0660.21997
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215488
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022665
X-RAY DIFFRACTIONr_nbd_refined0.1980.22959
X-RAY DIFFRACTIONr_nbd_other0.1870.210117
X-RAY DIFFRACTIONr_nbtor_refined0.170.26719
X-RAY DIFFRACTIONr_nbtor_other0.0820.26658
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.21154
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0960.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1340.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1310.230
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8781.511123
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.967213750
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.27636001
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.8874.54840
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A5583medium positional0.190.5
12C5583medium positional0.190.5
21B5621medium positional0.150.5
22D5621medium positional0.150.5
11A5583medium thermal0.432
12C5583medium thermal0.432
21B5621medium thermal0.492
22D5621medium thermal0.492
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.283 469
Rwork0.271 9058

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