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- PDB-2vjk: Formyl-CoA transferase with aspartyl-CoA thioester intermediate d... -

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Basic information

Entry
Database: PDB / ID: 2vjk
TitleFormyl-CoA transferase with aspartyl-CoA thioester intermediate derived from oxalyl-CoA
ComponentsFORMYL-COENZYME A TRANSFERASE
KeywordsTRANSFERASE / CYTOPLASM / 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
COENZYME A / Formyl-CoA:oxalate CoA-transferase
Similarity search - Component
Biological speciesOXALOBACTER FORMIGENES (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsBerthold, C.L. / Toyota, C.G. / Richards, N.G.J. / Lindqvist, Y.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Reinvestigation of the Catalytic Mechanism of Formyl-Coa Transferase, a Class III Coa-Transferase.
Authors: Berthold, C.L. / Toyota, C.G. / Richards, N.G.J. / Lindqvist, Y.
History
DepositionDec 11, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 25, 2007Provider: 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 / pdbx_struct_conn_angle / struct_conn
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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,3918
Polymers94,7262
Non-polymers1,6666
Water14,178787
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13760 Å2
ΔGint-99 kcal/mol
Surface area36470 Å2
MethodPQS
Unit cell
Length a, b, c (Å)151.906, 151.906, 99.504
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.8338, 0.48192, 0.2693), (0.48125, -0.87352, 0.07318), (0.27051, 0.06858, -0.96027)
Vector: -15.41757, 54.59987, 8.16578)

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Components

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


Mass: 47362.859 Da / Num. of mol.: 2
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-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 787 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
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 THIS RESIDUE 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: 2.71 Å3/Da / Density % sol: 54 % / 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: Mar 4, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2→56.08 Å / Num. obs: 75655 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 10.1
Reflection shellResolution: 2→2.11 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 2.4 / % possible all: 97.2

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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: 1.97→30 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.934 / SU B: 3.221 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.143 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.214 3910 5 %RANDOM
Rwork0.173 ---
obs0.175 74942 98.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.59 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å20 Å2
2--0.12 Å20 Å2
3----0.23 Å2
Refinement stepCycle: LAST / Resolution: 1.97→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6624 0 100 787 7511
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0226942
X-RAY DIFFRACTIONr_bond_other_d0.0010.024707
X-RAY DIFFRACTIONr_angle_refined_deg1.1161.9739427
X-RAY DIFFRACTIONr_angle_other_deg0.886311521
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6985876
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.39424.952315
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.479151178
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2151534
X-RAY DIFFRACTIONr_chiral_restr0.0720.21009
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.027762
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021340
X-RAY DIFFRACTIONr_nbd_refined0.1830.21423
X-RAY DIFFRACTIONr_nbd_other0.1820.25049
X-RAY DIFFRACTIONr_nbtor_refined0.1680.23337
X-RAY DIFFRACTIONr_nbtor_other0.0820.23304
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2613
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1390.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1790.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1230.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.41735543
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.60146859
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.33743130
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.8952556
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
LS refinement shellResolution: 1.97→2.02 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.298 257
Rwork0.258 5131

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