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- PDB-7kay: Crystal structure of OhyA(E82A)-18:1 complex from Staphylococcus ... -

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Basic information

Entry
Database: PDB / ID: 7kay
TitleCrystal structure of OhyA(E82A)-18:1 complex from Staphylococcus aureus
ComponentsOleate hydratase
KeywordsOXIDOREDUCTASE / Oleate hydratase / OhyA / SaOhyA / 18:1 / complex / oleic acid
Function / homology
Function and homology information


oleate hydratase / oleate hydratase activity / FAD binding / fatty acid metabolic process
Similarity search - Function
Oleate hydratase / MCRA family / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
: / OLEIC ACID / Myosin-cross-reactive antigen
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)210,61410
Polymers209,5043
Non-polymers1,1107
Water39,0392167
1
A: Oleate hydratase
hetero molecules

A: Oleate hydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,4978
Polymers139,6692
Non-polymers8276
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area7350 Å2
ΔGint-15 kcal/mol
Surface area43400 Å2
MethodPISA
2
B: Oleate hydratase
C: Oleate hydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,3656
Polymers139,6692
Non-polymers6964
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6850 Å2
ΔGint-12 kcal/mol
Surface area43090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)189.044, 113.534, 119.283
Angle α, β, γ (deg.)90.000, 117.040, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-947-

HOH

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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: Chemical ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C18H34O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: K
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2167 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.72 Å3/Da / Density % sol: 54.8 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Crystallized: 15% PEG 3000, 200 mM magnesium chloride, 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: Feb 6, 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: 1.95→29.459 Å / Num. obs: 150514 / % possible obs: 97.7 % / Redundancy: 3.5 % / Rpim(I) all: 0.041 / Net I/σ(I): 14
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 3.1 % / Num. unique obs: 10700 / Rpim(I) all: 0.399 / % possible all: 97.1

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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: 1.95→22.46 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 18.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1863 2001 1.33 %
Rwork0.1588 148478 -
obs0.1592 150479 92.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 84.91 Å2 / Biso mean: 24.8419 Å2 / Biso min: 7.91 Å2
Refinement stepCycle: final / Resolution: 1.95→22.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14085 0 189 2167 16441
Biso mean--34.32 37.99 -
Num. residues----1749
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00714503
X-RAY DIFFRACTIONf_angle_d0.79419631
X-RAY DIFFRACTIONf_dihedral_angle_d5.9198695
X-RAY DIFFRACTIONf_chiral_restr0.0522148
X-RAY DIFFRACTIONf_plane_restr0.0052514
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.95-1.99860.2604970.2044722963
1.9986-2.05260.21941110.1919858675
2.0526-2.1130.19411270.1806910279
2.113-2.18120.20251480.17521070194
2.1812-2.25910.1971490.17381117597
2.2591-2.34950.22791550.16931128998
2.3495-2.45640.22541440.17171127098
2.4564-2.58590.21271610.17011131098
2.5859-2.74780.19311460.1651129798
2.7478-2.95970.2061460.16431104196
2.9597-3.25720.19581580.15781127598
3.2572-3.72780.16561610.137611463100
3.7278-4.69350.13181460.12461141499
4.6935-22.460.17911520.17111132697

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