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- PDB-5egk: The structural and biochemical characterization of acyl-coa hydro... -

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Basic information

Entry
Database: PDB / ID: 5egk
TitleThe structural and biochemical characterization of acyl-coa hydrolase mutant Asp43Ala from Staphylococcus aureus
ComponentsAcyl CoA Hydrolase
KeywordsHYDROLASE / Acyl CoA thioesterase / Staphylococcus aureus / Coenzyme A / Hotdog thioesterase
Function / homology
Function and homology information


long-chain fatty acyl-CoA binding / acyl-CoA metabolic process / fatty acyl-CoA hydrolase activity / fatty acid metabolic process / cytosol
Similarity search - Function
Hotdog acyl-CoA thioesterase (ACOT)-type domain / Hotdog acyl-CoA thioesterase (ACOT)-type domain profile. / Cytosolic acyl coenzyme A thioester hydrolase / Thioesterase domain / Thioesterase superfamily / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
HotDog ACOT-type domain-containing protein
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsKhandokar, Y.B. / Srivastava, P.S. / Forwood, J.K.
CitationJournal: To Be Published
Title: The structural and biochemical characterization of acyl-coa hydrolase from Staphylococcus aureus
Authors: Khandokar, Y.B. / Srivastava, P.S. / Forwood, J.K.
History
DepositionOct 27, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2015Group: Structure summary
Revision 1.2Sep 27, 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 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acyl CoA Hydrolase
B: Acyl CoA Hydrolase
C: Acyl CoA Hydrolase
D: Acyl CoA Hydrolase
E: Acyl CoA Hydrolase
F: Acyl CoA Hydrolase


Theoretical massNumber of molelcules
Total (without water)121,3256
Polymers121,3256
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18650 Å2
ΔGint-119 kcal/mol
Surface area39850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.710, 129.000, 83.560
Angle α, β, γ (deg.)90.00, 104.10, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Acyl CoA Hydrolase


Mass: 20220.873 Da / Num. of mol.: 6 / Mutation: D43A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain Mu50 / ATCC 700699) (bacteria)
Strain: Mu50 / ATCC 700699 / Gene: SAV1878 / Plasmid: pMCSG21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)pLysS / References: UniProt: A0A0H3K033

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.34 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 1.6 M Ammonium Phosphate monobasic, 0.1 Sodium citrate tribasic pH 4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 31, 2015
RadiationMonochromator: SILICON DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.4→29.96 Å / Num. obs: 39444 / % possible obs: 98.88 % / Redundancy: 2 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 7.63
Reflection shellResolution: 2.4→2.486 Å / Redundancy: 2 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.1 / % possible all: 98.62

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Processing

Software
NameVersionClassification
PHENIX(1.10pre_2104: ???)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NCP

4ncp


Resolution: 2.4→29.96 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 24.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2384 1919 4.87 %
Rwork0.2065 --
obs0.2081 39432 98.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→29.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7831 0 0 0 7831
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087993
X-RAY DIFFRACTIONf_angle_d1.22410812
X-RAY DIFFRACTIONf_dihedral_angle_d15.3642974
X-RAY DIFFRACTIONf_chiral_restr0.1621207
X-RAY DIFFRACTIONf_plane_restr0.0061396
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.460.30951280.27592680X-RAY DIFFRACTION99
2.46-2.52650.3581400.28222645X-RAY DIFFRACTION99
2.5265-2.60080.32091120.27762699X-RAY DIFFRACTION99
2.6008-2.68470.31541320.26312673X-RAY DIFFRACTION99
2.6847-2.78060.28111150.25362706X-RAY DIFFRACTION99
2.7806-2.89180.27261600.25112656X-RAY DIFFRACTION99
2.8918-3.02330.28141460.24322616X-RAY DIFFRACTION99
3.0233-3.18250.27111480.22842672X-RAY DIFFRACTION99
3.1825-3.38170.24461440.21582682X-RAY DIFFRACTION99
3.3817-3.64240.26061660.20812651X-RAY DIFFRACTION99
3.6424-4.00810.1841350.1852679X-RAY DIFFRACTION99
4.0081-4.58630.19381360.16062710X-RAY DIFFRACTION99
4.5863-5.77150.18291440.16312698X-RAY DIFFRACTION99
5.7715-29.96690.21161130.18132746X-RAY DIFFRACTION98

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