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

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Basic information

Entry
Database: PDB / ID: 5egj
TitleThe structural and biochemical characterization of acyl-coa hydrolase mutant Asn28Ala from Staphylococcus aureus in complex with COENZYME A
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
COENZYME A / 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 1.2Dec 16, 2015Group: Other
Revision 1.3Sep 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9892
Polymers20,2221
Non-polymers7681
Water1267
1
A: Acyl CoA Hydrolase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)125,93612
Polymers121,3316
Non-polymers4,6056
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
crystal symmetry operation10_444-y-1,-x-1,-z-1/21
crystal symmetry operation11_554-x+y,y,-z-1/21
crystal symmetry operation12_544x,x-y-1,-z-1/21
Buried area26090 Å2
ΔGint-99 kcal/mol
Surface area38750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.730, 127.730, 55.722
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-304-

HOH

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Components

#1: Protein Acyl CoA Hydrolase


Mass: 20221.857 Da / Num. of mol.: 1
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
#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.29 Å3/Da / Density % sol: 62 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M Sodium HEPES pH7.5, 0.8 M Sodium phosphate monobasic

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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→33.44 Å / Num. obs: 10919 / % possible obs: 99.93 % / Redundancy: 2 % / Rmerge(I) obs: 0.02896 / Net I/σ(I): 8.73
Reflection shellResolution: 2.4→2.486 Å / Redundancy: 2 % / Rmerge(I) obs: 0.09755 / Mean I/σ(I) obs: 3.61 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXdev_1894refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NCP

4ncp


Resolution: 2.4→33.44 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2571 568 5.2 %
Rwork0.2075 --
obs0.21 10914 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.6 Å2
Refinement stepCycle: LAST / Resolution: 2.4→33.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1319 0 48 7 1374
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081396
X-RAY DIFFRACTIONf_angle_d1.0411896
X-RAY DIFFRACTIONf_dihedral_angle_d15.772511
X-RAY DIFFRACTIONf_chiral_restr0.035208
X-RAY DIFFRACTIONf_plane_restr0.005239
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4001-2.64150.31281390.25082516X-RAY DIFFRACTION100
2.6415-3.02350.33881430.2422533X-RAY DIFFRACTION100
3.0235-3.80850.27481500.21352559X-RAY DIFFRACTION100
3.8-33.440.20091360.18022738X-RAY DIFFRACTION100

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