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- PDB-5hz4: The structural and biochemical characterization of acyl-coa hydro... -

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Basic information

Entry
Database: PDB / ID: 5hz4
TitleThe structural and biochemical characterization of acyl-coa hydrolase mutant Thr60Ala from Staphylococcus aureus.
ComponentsThioesterase
KeywordsHYDROLASE / Thioesterase / Staphylococcus aureus / 4HBT
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. / Forwood, J.K.
CitationJournal: To Be Published
Title: The structural and biochemical characterization of acyl-coa hydrolase mutant Thr60Ala from Staphylococcus aureus.
Authors: Khandokar, Y.B. / Srivastava, P. / Forwood, J.K.
History
DepositionFeb 2, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 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

Downloads & links

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Assembly

Deposited unit
A: Thioesterase
B: Thioesterase
C: Thioesterase
D: Thioesterase
E: Thioesterase
F: Thioesterase


Theoretical massNumber of molelcules
Total (without water)121,4096
Polymers121,4096
Non-polymers00
Water93752
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17380 Å2
ΔGint-109 kcal/mol
Surface area37910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.050, 128.540, 84.360
Angle α, β, γ (deg.)90.00, 104.20, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Thioesterase


Mass: 20234.855 Da / Num. of mol.: 6 / Mutation: T60A
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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.16 Å3/Da / Density % sol: 43.15 %
Crystal growTemperature: 296 K / Method: vapor diffusion / pH: 8.5
Details: 30% PEG4000, 0.1M tris pH 8.5, 0.2 M lithium sulfate

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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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.5→31.7 Å / Num. obs: 35749 / % possible obs: 99.9 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.122 / Net I/σ(I): 9.6
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.67 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NCP

4ncp


Resolution: 2.5→31.7 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.886 / SU B: 0.007 / SU ML: 0 / Cross valid method: THROUGHOUT / ESU R: 0.285 / ESU R Free: 0.342 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28297 1700 4.8 %RANDOM
Rwork0.23551 ---
obs0.23786 34019 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 48.189 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å20.07 Å2
2---0.92 Å20 Å2
3---0.71 Å2
Refinement stepCycle: 1 / Resolution: 2.5→31.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7639 0 0 52 7691
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 120 -
Rwork0.305 2502 -
obs--99.92 %

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