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- PDB-5eo2: Structural and biochemical characterization of the hypothetical p... -

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Basic information

Entry
Database: PDB / ID: 5eo2
TitleStructural and biochemical characterization of the hypothetical protein SAV2348 from Staphylococcus aureus in complex with CoA.
Componentsthioesterase
KeywordsHYDROLASE / Thioesterases / hypothetical protein SAV2348 / staphylococcus aureus / coenzyme A
Function / homologyThioesterase-like superfamily / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta / COENZYME A / Thioesterase / Thioesterase
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsKhandokar, Y.B. / Srivastava, P. / Forwood, J.K.
CitationJournal: To Be Published
Title: Structural and biochemical characterization of the hypothetical protein SAV2348 from Staphylococcus aureus in complex with CoA
Authors: Khandokar, Y.B. / Srivastava, P. / Forwood, J.K.
History
DepositionNov 10, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / 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
B: thioesterase
C: thioesterase
D: thioesterase
E: thioesterase
F: thioesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,31612
Polymers114,7116
Non-polymers4,6056
Water3,783210
1
A: thioesterase
D: thioesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7724
Polymers38,2372
Non-polymers1,5352
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5180 Å2
ΔGint-12 kcal/mol
Surface area12890 Å2
MethodPISA
2
B: thioesterase
C: thioesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7724
Polymers38,2372
Non-polymers1,5352
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5850 Å2
ΔGint-8 kcal/mol
Surface area14930 Å2
MethodPISA
3
E: thioesterase
F: thioesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7724
Polymers38,2372
Non-polymers1,5352
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5810 Å2
ΔGint-12 kcal/mol
Surface area14960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.980, 127.630, 97.680
Angle α, β, γ (deg.)90.00, 93.71, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
thioesterase


Mass: 19118.453 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain Mu50 / ATCC 700699) (bacteria)
Strain: Mu50 / ATCC 700699 / Gene: SAV2348 / Plasmid: pMCSG21 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): pLysS / References: UniProt: A0A0H3JRH2, UniProt: A0A0H3JSY9*PLUS
#2: Chemical
ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / 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: 2.6 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 0.1M sodium acetate pH4.6, 2M Ammonium 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: Jul 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.5→97.48 Å / Num. obs: 37843 / % possible obs: 99.55 % / Redundancy: 2 % / Net I/σ(I): 8.73

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 2.5→97.48 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.895 / SU B: 0.005 / SU ML: 0 / Cross valid method: THROUGHOUT / ESU R: 0.25 / ESU R Free: 0.29 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24575 1821 4.8 %RANDOM
Rwork0.21168 ---
obs0.21337 36022 99.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.809 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å2-0.01 Å2
2---0.02 Å2-0 Å2
3---0.03 Å2
Refinement stepCycle: 1 / Resolution: 2.5→97.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7262 0 288 210 7760
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 129 -
Rwork0.286 2627 -
obs--99.6 %

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