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- PDB-1t4c: Formyl-CoA Transferase in complex with Oxalyl-CoA -

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Basic information

Entry
Database: PDB / ID: 1t4c
TitleFormyl-CoA Transferase in complex with Oxalyl-CoA
ComponentsFormyl-CoA:oxalate CoA-transferase
KeywordsTRANSFERASE / CoA transferase / oxalate / oxalate degradation / intertwined / knotted fold / CAIB-BAIF family / Oxalyl-CoA / anhydride
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 / OXALIC ACID / Formyl-CoA:oxalate CoA-transferase
Similarity search - Component
Biological speciesOxalobacter formigenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 Å
AuthorsRicagno, S. / Jonsson, S. / Richards, N.G. / Lindqvist, Y.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Kinetic and mechanistic characterization of the formyl-CoA transferase from Oxalobacter formigenes
Authors: Jonsson, S. / Ricagno, S. / Lindqvist, Y. / Richards, N.G.
History
DepositionApr 29, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 3, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.3Aug 8, 2018Group: Advisory / Data collection / Source and taxonomy
Category: diffrn_source / entity_src_gen / pdbx_unobs_or_zero_occ_residues
Item: _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 2.0Apr 12, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Other / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / cell ...atom_site / cell / chem_comp / database_2 / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_mod_residue / pdbx_unobs_or_zero_occ_residues / pdbx_validate_rmsd_bond / pdbx_validate_torsion / struct_asym / struct_conf / struct_conn / struct_ncs_dom_lim / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.occupancy / _atom_site.type_symbol / _cell.Z_PDB / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_ec / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_entry_details.sequence_details / _pdbx_poly_seq_scheme.entity_id / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_torsion.auth_comp_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.ref_id / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site.pdbx_num_residues
Revision 2.1Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.2Oct 9, 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-CoA:oxalate CoA-transferase
B: Formyl-CoA:oxalate CoA-transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,0885
Polymers94,4632
Non-polymers1,6253
Water2,342130
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14990 Å2
ΔGint-78 kcal/mol
Surface area29840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.163, 100.163, 196.872
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRALAALA2AA2 - 1501 - 149
21THRTHRALAALA2BB2 - 1501 - 149
12HISHISSERSER2AA175 - 250174 - 249
22HISHISSERSER2BB175 - 250174 - 249
13VALVALVALVAL4AA280 - 428279 - 427
23VALVALVALVAL4BB280 - 428279 - 427

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Formyl-CoA:oxalate CoA-transferase / FCOCT / Formyl-coenzyme A transferase


Mass: 47231.668 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oxalobacter formigenes (bacteria) / Gene: frc / Plasmid: pET9a / Production host: Escherichia coli BL21(DE3) (bacteria) / 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 / References: UniProt: O06644*PLUS
#3: Chemical ChemComp-OXD / OXALIC ACID


Mass: 90.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H2O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE AUTHOR SAID THAT THE AMINO ACID AT POSITION 186 IS ILE, THE SWS IS INCORRECT.

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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: 2.57 Å3/Da / Density % sol: 51.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Mg acetate, PEG 8000, Na cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.087 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 8, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.087 Å / Relative weight: 1
ReflectionResolution: 2.61→25.48 Å / Num. all: 30208 / Num. obs: 30208 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Biso Wilson estimate: 63.4 Å2 / Rsym value: 0.118 / Net I/σ(I): 15.6
Reflection shellResolution: 2.6→2.67 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 4.6 / Num. unique all: 4046 / Rsym value: 0.332 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1P5R

1p5r


Resolution: 2.61→20 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.899 / SU B: 11.384 / SU ML: 0.243 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 1.242 / ESU R Free: 0.358 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27308 1514 5 %RANDOM
Rwork0.20001 ---
all0.20369 30208 --
obs0.20369 28694 96.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 30.374 Å2
Baniso -1Baniso -2Baniso -3
1--2.78 Å20 Å20 Å2
2---2.78 Å20 Å2
3---5.56 Å2
Refinement stepCycle: LAST / Resolution: 2.61→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6631 0 96 130 6857
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0216872
X-RAY DIFFRACTIONr_bond_other_d0.0020.026120
X-RAY DIFFRACTIONr_angle_refined_deg1.8211.9689306
X-RAY DIFFRACTIONr_angle_other_deg0.96314302
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.375850
X-RAY DIFFRACTIONr_chiral_restr0.1040.2988
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027643
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021321
X-RAY DIFFRACTIONr_nbd_refined0.2210.21542
X-RAY DIFFRACTIONr_nbd_other0.2380.27249
X-RAY DIFFRACTIONr_nbtor_other0.0950.24068
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.2195
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1610.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1780.223
X-RAY DIFFRACTIONr_mcbond_it0.7621.54224
X-RAY DIFFRACTIONr_mcangle_it1.42526773
X-RAY DIFFRACTIONr_scbond_it1.98432648
X-RAY DIFFRACTIONr_scangle_it3.3234.52533
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
1872tight positional0.060.05
2443tight positional0.060.05
11340medium positional0.60.5
2729medium positional0.590.5
32275medium positional0.530.5
1872tight thermal0.150.5
2443tight thermal0.140.5
11340medium thermal0.682
2729medium thermal0.652
32275medium thermal0.732
LS refinement shellResolution: 2.609→2.677 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.331 79
Rwork0.29 2016
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5633-0.0980.05860.0775-0.13270.53190.07930.0542-0.0388-0.058-0.0613-0.01940.11270.1291-0.0180.1360.063600.32390.02590.139180.5867.9710.176
210.1825-0.8294-0.77771.260.16840.19810.33870.4779-0.5046-0.4147-0.13540.4112-0.06150.0627-0.20330.13180.1091-0.11370.2052-0.040.123749.76331.1130.922
31.0945-0.37130.45050.414-0.14470.4180.0863-0.04120.06210.0583-0.1028-0.0559-0.01610.0990.01650.08880.02310.00010.32910.0150.109177.71418.52622.891
40.3613-0.04670.09490.2624-0.060.47530.0412-0.02540.0161-0.0630.0019-0.01320.0448-0.0329-0.04310.1070.0185-0.01110.2705-0.010.17965.74812.92812.568
512.66432.56850.54260.13052.11946.4474-0.22830.46190.0853-0.36140.0863-0.1607-0.9030.56230.1420.26950.0232-0.01120.2628-0.01010.2586103.1921.503-4.192
60.5133-0.3569-0.25370.17870.10590.78330.04020.1864-0.1836-0.1188-0.007-0.09340.2108-0.0564-0.03320.16040.0276-0.03830.2661-0.02950.18968.5813.432-0.955
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 280
2X-RAY DIFFRACTION2A281 - 315
3X-RAY DIFFRACTION3A316 - 428
4X-RAY DIFFRACTION4B2 - 280
5X-RAY DIFFRACTION5B281 - 315
6X-RAY DIFFRACTION6B316 - 428

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