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- PDB-2g04: Crystal structure of fatty acid-CoA racemase from Mycobacterium t... -

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Basic information

Entry
Database: PDB / ID: 2g04
TitleCrystal structure of fatty acid-CoA racemase from Mycobacterium tuberculosis H37Rv
ComponentsPROBABLE FATTY-ACID-CoA RACEMASE FAR
KeywordsISOMERASE
Function / homology
Function and homology information


CoA-transferase activity / plasma membrane
Similarity search - Function
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 / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Fatty acid-CoA racemase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsLee, K.S. / Park, S.M. / Rhee, K.H. / Bang, W.G. / Hwang, K.Y. / Chi, Y.M.
CitationJournal: Proteins / Year: 2006
Title: Crystal structure of fatty acid-CoA racemase from Mycobacterium tuberculosis H37Rv
Authors: Lee, K.S. / Park, S.M. / Rhee, K.H. / Bang, W.G. / Hwang, K.Y. / Chi, Y.M.
History
DepositionFeb 11, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 2, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROBABLE FATTY-ACID-CoA RACEMASE FAR
B: PROBABLE FATTY-ACID-CoA RACEMASE FAR
C: PROBABLE FATTY-ACID-CoA RACEMASE FAR
D: PROBABLE FATTY-ACID-CoA RACEMASE FAR
E: PROBABLE FATTY-ACID-CoA RACEMASE FAR
F: PROBABLE FATTY-ACID-CoA RACEMASE FAR


Theoretical massNumber of molelcules
Total (without water)228,5676
Polymers228,5676
Non-polymers00
Water8,503472
1
A: PROBABLE FATTY-ACID-CoA RACEMASE FAR
B: PROBABLE FATTY-ACID-CoA RACEMASE FAR


Theoretical massNumber of molelcules
Total (without water)76,1892
Polymers76,1892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12530 Å2
ΔGint-100 kcal/mol
Surface area24720 Å2
MethodPISA
2
C: PROBABLE FATTY-ACID-CoA RACEMASE FAR
D: PROBABLE FATTY-ACID-CoA RACEMASE FAR


Theoretical massNumber of molelcules
Total (without water)76,1892
Polymers76,1892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12520 Å2
ΔGint-99 kcal/mol
Surface area24750 Å2
MethodPISA
3
E: PROBABLE FATTY-ACID-CoA RACEMASE FAR
F: PROBABLE FATTY-ACID-CoA RACEMASE FAR


Theoretical massNumber of molelcules
Total (without water)76,1892
Polymers76,1892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12530 Å2
ΔGint-100 kcal/mol
Surface area24990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.562, 109.562, 147.973
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein
PROBABLE FATTY-ACID-CoA RACEMASE FAR


Mass: 38094.441 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: far / Plasmid: pET-28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O53867, alpha-methylacyl-CoA racemase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 472 / 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: 2.24 Å3/Da / Density % sol: 45.13 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 20% PEG 4000, 0.2M Amm, chloride, 0.01M Ca, chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6B / Wavelength: 1.12714 Å
DetectorType: BRUKER PROTEUM 300 / Detector: CCD / Date: Dec 4, 2005
RadiationMonochromator: Double Crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12714 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 52589 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 35 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 9.9
Reflection shellResolution: 2.7→2.82 Å / Redundancy: 4 % / Mean I/σ(I) obs: 2 / Num. unique all: 5942 / Rsym value: 0.306 / % possible all: 86.2

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1X74

1x74


Resolution: 2.7→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.29 2668 -RANDOM
Rwork0.24 ---
obs0.24 52309 95.9 %-
all-54526 --
Displacement parametersBiso mean: 55.9 Å2
Baniso -1Baniso -2Baniso -3
1-10.8 Å212.4 Å20 Å2
2--10.8 Å20 Å2
3----21.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.53 Å0.43 Å
Luzzati d res low-5 Å
Luzzati sigma a0.93 Å0.81 Å
Refinement stepCycle: LAST / Resolution: 2.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15756 0 0 472 16228
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_improper_angle_d0.88
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.006
RfactorNum. reflection% reflection
Rfree0.42 2668 -
Rwork0.4 --
obs-52309 87.3 %

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