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- PDB-1p5r: Formyl-CoA Transferase in complex with Coenzyme A -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1p5r
TitleFormyl-CoA Transferase in complex with Coenzyme A
ComponentsFormyl-coenzyme A transferase
KeywordsTRANSFERASE / CoA-transferase / oxalate / oxalate degradation / intertwined / knotted fold / CAIB-BAIF family / CoA complex
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 / FOURIER SYNTHESIS / Resolution: 2.5 Å
AuthorsRicagno, S. / Jonsson, S. / Richards, N. / Lindqvist, Y.
CitationJournal: Embo J. / Year: 2003
Title: Formyl-CoA Transferase encloses the CoA binding site at the interface of an interlocked dimer
Authors: Ricagno, S. / Jonsson, S. / Richards, N. / Lindqvist, Y.
History
DepositionApr 28, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,2974
Polymers94,7622
Non-polymers1,5352
Water4,720262
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14890 Å2
ΔGint-90 kcal/mol
Surface area29250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.400, 151.400, 99.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

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


Mass: 47380.895 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oxalobacter formigenes (bacteria) / Gene: FRC / Plasmid: pET9a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)
References: UniProt: O06644, Transferases; Transferring sulfur-containing groups; CoA-transferases
#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / Source method: isolated from a natural source / Formula: H2O

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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: 3.01 Å3/Da / Density % sol: 59.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 4000, Magnesium cloride, Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: Ricagno, S., (2003) Acta Crystallogr., D59, 1276.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
17.5 mg/mlprotein1drop
226 %PEG40001reservoir
3100 mMHEPES1reservoirpH7.5
40.5 M1reservoirMgCl2

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 21, 2002
RadiationMonochromator: Si(311) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.5→29.79 Å / Num. all: 38678 / Num. obs: 38678 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 49.6 Å2 / Limit h max: 60 / Limit h min: 0 / Limit k max: 60 / Limit k min: 0 / Limit l max: 39 / Limit l min: 0 / Observed criterion F max: 2462972.14 / Observed criterion F min: 23 / Rsym value: 0.085 / Net I/σ(I): 16.4
Reflection shellResolution: 2.5→2.65 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 4.2 / Rsym value: 0.219 / % possible all: 98.1
Reflection
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 25 Å / Rmerge(I) obs: 0.164
Reflection shell
*PLUS
% possible obs: 98.1 % / Rmerge(I) obs: 0.042 / Mean I/σ(I) obs: 3.1

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1P5H

1p5h


Resolution: 2.5→24.88 Å / Rfactor Rfree error: 0.005 / Occupancy max: 1 / Occupancy min: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: maximum likelihood
RfactorNum. reflection% reflectionSelection details
Rfree0.236 1901 4.9 %random
Rwork0.194 ---
obs0.194 38641 99.3 %-
all-38907 --
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 31.32712 Å2 / ksol: 0.332133 e/Å3
Displacement parametersBiso max: 119.44 Å2 / Biso mean: 47.38 Å2 / Biso min: 12.38 Å2
Baniso -1Baniso -2Baniso -3
1--1.71 Å20 Å20 Å2
2---1.71 Å20 Å2
3---3.41 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.21 Å
Luzzati d res high-2.5
Refinement stepCycle: LAST / Resolution: 2.5→24.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6624 0 96 262 6982
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_torsion_deg22.6
X-RAY DIFFRACTIONc_torsion_impr_deg0.85
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.5-2.610.2942525.50.25343350.0184850458794.6
2.61-2.750.2652485.10.22245790.0174833482799.9
2.75-2.920.2432204.60.20846130.0164841483399.8
2.92-3.150.2672324.80.20646150.01848474847100
3.15-3.460.2532585.30.20145980.0164862485699.9
3.46-3.960.24924350.20446310.0164876487499.9
3.96-4.990.1992154.40.16446520.0144871486799.9
4.99-24.880.2052334.70.17947170.01349524950100
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2carbohydrate.param
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4ion.paramprotein.top
X-RAY DIFFRACTION5CoA.paramCoA.top

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