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- PDB-7kax: Crystal structure of OhyA(E82A) from Staphylococcus aureus -

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Basic information

Entry
Database: PDB / ID: 7kax
TitleCrystal structure of OhyA(E82A) from Staphylococcus aureus
ComponentsOleate hydratase
KeywordsOXIDOREDUCTASE / Oleate hydratase / OhyA / SaOhyA
Function / homologyoleate hydratase / oleate hydratase activity / Oleate hydratase / MCRA family / FAD binding / fatty acid metabolic process / FAD/NAD(P)-binding domain superfamily / Myosin-cross-reactive antigen
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.514 Å
AuthorsRadka, C.D. / Rock, C.O.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM034496 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA21765 United States
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Structure and mechanism of Staphylococcus aureus oleate hydratase (OhyA).
Authors: Radka, C.D. / Batte, J.L. / Frank, M.W. / Young, B.M. / Rock, C.O.
History
DepositionOct 1, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 6, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2021Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Apr 28, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Oleate hydratase
B: Oleate hydratase
C: Oleate hydratase


Theoretical massNumber of molelcules
Total (without water)209,5043
Polymers209,5043
Non-polymers00
Water1629
1
A: Oleate hydratase

A: Oleate hydratase


Theoretical massNumber of molelcules
Total (without water)139,6692
Polymers139,6692
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area4740 Å2
ΔGint-16 kcal/mol
Surface area44060 Å2
MethodPISA
2
B: Oleate hydratase
C: Oleate hydratase


Theoretical massNumber of molelcules
Total (without water)139,6692
Polymers139,6692
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4620 Å2
ΔGint-17 kcal/mol
Surface area44490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)189.669, 113.876, 119.756
Angle α, β, γ (deg.)90.000, 117.230, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Oleate hydratase / Myosin-cross-reactive antigen


Mass: 69834.688 Da / Num. of mol.: 3 / Mutation: E82A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria)
Gene: DD547_00094, DQV53_00770, EP54_06595, EQ90_12415, G0V24_00735, G0X12_00605, G0Z18_00840, G6Y10_10285, GO746_00220, GO803_11440, GO805_08895, GO821_10135, GO894_07145, GO942_14045, HMPREF3211_ ...Gene: DD547_00094, DQV53_00770, EP54_06595, EQ90_12415, G0V24_00735, G0X12_00605, G0Z18_00840, G6Y10_10285, GO746_00220, GO803_11440, GO805_08895, GO821_10135, GO894_07145, GO942_14045, HMPREF3211_02399, NCTC10654_00136, RK64_00980
Production host: Escherichia coli (E. coli) / References: UniProt: A0A0D6GJV1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.74 Å3/Da / Density % sol: 55.18 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Crystallization: 15% PEG 3000, 200 mM magnesium chloride, and 100 mM sodium cacodylate, pH 6.5. Cryo: 15% PEG 3000, 200 mM magnesium chloride, 100 mM sodium cacodylate, pH 6.5, 30% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 8, 2020
RadiationMonochromator: Si 111. Rosenbaum-Rock double-crystal monochromator: liquid nitrogen cooled; sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.51→30.122 Å / Num. obs: 50990 / % possible obs: 97.7 % / Redundancy: 3.8 % / Rpim(I) all: 0.072 / Net I/σ(I): 8.4
Reflection shellResolution: 3.51→3.56 Å / Redundancy: 3.2 % / Num. unique obs: 2483 / Rpim(I) all: 0.17 / % possible all: 94.6

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7KAV

7kav


Resolution: 3.514→30.122 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2486 3707 7.27 %
Rwork0.1857 47283 -
obs0.1904 50990 91.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 130.26 Å2 / Biso mean: 49.8328 Å2 / Biso min: 19.69 Å2
Refinement stepCycle: final / Resolution: 3.514→30.122 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13912 0 0 9 13921
Biso mean---31.74 -
Num. residues----1743
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00314264
X-RAY DIFFRACTIONf_angle_d0.53319359
X-RAY DIFFRACTIONf_dihedral_angle_d4.6268509
X-RAY DIFFRACTIONf_chiral_restr0.0432145
X-RAY DIFFRACTIONf_plane_restr0.0042484
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.5141-3.56030.2974970.2304127763
3.5603-3.6090.29861210.2294138872
3.609-3.66050.32521110.2185155277
3.6605-3.7150.26461450.2171165285
3.715-3.7730.30381290.2056174488
3.773-3.83470.27021580.1988183091
3.8347-3.90070.25191290.1902183294
3.9007-3.97150.2541620.1879189795
3.9715-4.04770.27671270.196184895
4.0477-4.13010.27551320.1787194396
4.1301-4.21970.23751590.1698190997
4.2197-4.31750.18941520.1742185096
4.3175-4.42520.27141390.18196897
4.4252-4.54440.25551720.1803187796
4.5444-4.67770.29431430.1731191397
4.6777-4.82810.2411560.1685186795
4.8281-4.99990.23491470.1766195997
4.9999-5.19910.2491570.1664189097
5.1991-5.43440.24461430.1805191998
5.4344-5.71910.22651630.1804194498
5.7191-6.07470.23681520.1831190297
6.0747-6.53930.24581370.1966191797
6.5393-7.18930.25431410.1893171387
7.1893-8.21110.2321530.1786192297
8.2111-10.27640.18621390.1651191996
10.2764-30.1220.22641430.1995185194

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