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- PDB-1p5h: Crystal structure of Formyl-CoA Transferase (apoenzyme) from Oxal... -

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Basic information

Entry
Database: PDB / ID: 1p5h
TitleCrystal structure of Formyl-CoA Transferase (apoenzyme) from Oxalobacter formigenes
ComponentsFormyl-coenzyme A transferase
KeywordsTRANSFERASE / CoA-transferase / oxalate / oxalate degradation / intertwined / knotted fold / CAIB-BAIF family
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 / CoA-transferase family III domain 3 superfamily / formyl-coa transferase, domain 3 / CoA-transferase family III / CoA-transferase family III domain 1 superfamily / CoA-transferase family III / Rossmann fold / 2-Layer Sandwich ...Formyl-CoA:oxalate CoA-transferase / formyl-coa transferase, domain 3 / Crotonobetainyl-coa:carnitine coa-transferase; domain 1 / CoA-transferase family III domain 3 superfamily / formyl-coa transferase, domain 3 / CoA-transferase family III / CoA-transferase family III domain 1 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 / SAD / Resolution: 2.2 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 27, 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: Advisory / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site

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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


Theoretical massNumber of molelcules
Total (without water)94,7622
Polymers94,7622
Non-polymers00
Water9,548530
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12400 Å2
ΔGint-87 kcal/mol
Surface area30690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.440, 151.440, 99.490
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 530 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.01 Å3/Da / Density % sol: 59.11 %
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

Diffraction
IDMean temperature (K)Crystal-ID
11101
21101
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID14-110.933
SYNCHROTRONEMBL/DESY, HAMBURG BW7A20.979
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 41CCDDec 9, 2001
MAR CCD 165 mm2CCDJun 8, 2002Premirror, double crystal focussing monochromator, bent mirror
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Diamond (111), Ge (220)SINGLE WAVELENGTHMx-ray1
2Double crystal focussing monochromatorSADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9331
20.9791
ReflectionResolution: 2.2→25 Å / Num. all: 53823 / Num. obs: 53823 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Rsym value: 0.098 / Net I/σ(I): 15.3
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 4.9 / Rsym value: 0.236 / % possible all: 99
Reflection
*PLUS
Num. obs: 57045 / % possible obs: 99 % / Rmerge(I) obs: 0.098
Reflection shell
*PLUS
% possible obs: 99 % / Rmerge(I) obs: 0.236

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→24.62 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.927 / SU B: 4.364 / SU ML: 0.113 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.204 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20902 2870 5.1 %RANDOM
Rwork0.17108 ---
obs0.17295 53823 100 %-
all-53823 --
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: 30.915 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.2→24.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6624 0 0 530 7154
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0216767
X-RAY DIFFRACTIONr_bond_other_d0.0020.026063
X-RAY DIFFRACTIONr_angle_refined_deg1.2971.959150
X-RAY DIFFRACTIONr_angle_other_deg0.829314170
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0935850
X-RAY DIFFRACTIONr_chiral_restr0.0830.2980
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027594
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021320
X-RAY DIFFRACTIONr_nbd_refined0.1920.21412
X-RAY DIFFRACTIONr_nbd_other0.2320.27032
X-RAY DIFFRACTIONr_nbtor_other0.0860.23840
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.2423
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0830.24
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1650.224
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.180.212
X-RAY DIFFRACTIONr_mcbond_it0.7191.54223
X-RAY DIFFRACTIONr_mcangle_it1.34926772
X-RAY DIFFRACTIONr_scbond_it1.82232544
X-RAY DIFFRACTIONr_scangle_it34.52378
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.224 193
Rwork0.177 3749
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)
10.8176-0.026-0.31030.4666-0.13970.6963-0.0413-0.0307-0.0370.12250.03230.0826-0.0389-0.11170.0090.05480.04240.02220.06650.00310.0423-36.51221.948.439
20.5235-0.1102-0.03540.69320.33381.01540.0093-0.0182-0.002-0.00140.02720.0942-0.0549-0.1204-0.03650.03330.02830.01280.030.02490.0378-34.4117.6720.645
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 4282 - 428
2X-RAY DIFFRACTION2BB2 - 4282 - 428
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 25 Å / Rfactor Rfree: 0.209 / Rfactor Rwork: 0.171
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor Rfree: 0.219 / Rfactor Rwork: 0.19

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