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

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Basic information

Entry
Database: PDB / ID: 5hwf
TitleThe structural and biochemical characterization of acyl-coa hydrolase mutant Asn28Ala from Staphylococcus aureus.
ComponentsThioesterase
KeywordsHYDROLASE / Acyl CoA thioesterase / Staphylococcus aureus / Coenzyme A / Hotdog thioesterase
Function / homology
Function and homology information


long-chain fatty acyl-CoA hydrolase activity / acyl-CoA metabolic process / fatty acid catabolic process / cytosol
Similarity search - Function
Hotdog acyl-CoA thioesterase (ACOT)-type domain / Cytosolic acyl coenzyme A thioester hydrolase / Hotdog acyl-CoA thioesterase (ACOT)-type domain profile. / 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: 2.5 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
DepositionJan 29, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 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_prerelease_seq / 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

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Assembly

Deposited unit
A: Thioesterase


Theoretical massNumber of molelcules
Total (without water)20,2221
Polymers20,2221
Non-polymers00
Water00
1
A: Thioesterase
x 6


Theoretical massNumber of molelcules
Total (without water)121,3316
Polymers121,3316
Non-polymers00
Water0
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 area18470 Å2
ΔGint-119 kcal/mol
Surface area40070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.310, 127.310, 55.610
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein Thioesterase


Mass: 20221.857 Da / Num. of mol.: 1 / Mutation: N28A
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) / References: UniProt: A0A0H3K033

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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: 3.21 Å3/Da / Density % sol: 61.68 %
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 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.5→31.83 Å / Num. obs: 9615 / % possible obs: 99.9 % / Redundancy: 15.9 % / Net I/σ(I): 8.7
Reflection shellResolution: 2.5→2.6 Å / Rmerge(I) obs: 0.192

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NCP

4ncp


Resolution: 2.5→30.66 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.903 / SU B: 0.006 / SU ML: 0 / Cross valid method: THROUGHOUT / ESU R: 0.234 / ESU R Free: 0.267 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27584 484 5 %RANDOM
Rwork0.24152 ---
obs0.24321 9131 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 54.635 Å2
Baniso -1Baniso -2Baniso -3
1--2.3 Å2-1.15 Å2-0 Å2
2---2.3 Å20 Å2
3---7.47 Å2
Refinement stepCycle: 1 / Resolution: 2.5→30.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1319 0 0 0 1319
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 37 -
Rwork0.329 650 -
obs--100 %

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