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- PDB-7kaz: Crystal structure of OhyA(E82A)-18:1/h18:0-FAD complex from Staph... -

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Basic information

Entry
Database: PDB / ID: 7kaz
TitleCrystal structure of OhyA(E82A)-18:1/h18:0-FAD complex from Staphylococcus aureus
ComponentsOleate hydratase
KeywordsOXIDOREDUCTASE / Oleate hydratase / OhyA / SaOhyA / 18:1 / complex / oleic acid / hydroxystearic acid / FAD / h18:0
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
FLAVIN-ADENINE DINUCLEOTIDE / : / OLEIC ACID / (10R)-10-hydroxyoctadecanoic acid / Myosin-cross-reactive antigen
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.854 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
C: Oleate hydratase
B: Oleate hydratase
A: Oleate hydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)211,9809
Polymers209,5043
Non-polymers2,4766
Water49,0912725
1
C: Oleate hydratase
A: Oleate hydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,0776
Polymers139,6692
Non-polymers1,4084
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7120 Å2
ΔGint-21 kcal/mol
Surface area42040 Å2
MethodPISA
2
B: Oleate hydratase
hetero molecules

B: Oleate hydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,8056
Polymers139,6692
Non-polymers2,1364
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area9430 Å2
ΔGint-22 kcal/mol
Surface area41690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)188.022, 113.085, 118.393
Angle α, β, γ (deg.)90.000, 116.910, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-1613-

HOH

21B-943-

HOH

31B-1362-

HOH

41B-1604-

HOH

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Components

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Protein , 1 types, 3 molecules CBA

#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

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Non-polymers , 5 types, 2731 molecules

#2: Chemical ChemComp-WAD / (10R)-10-hydroxyoctadecanoic acid / (R)-10-Hydroxystearic acid


Mass: 300.477 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H36O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H34O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2725 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.68 Å3/Da / Density % sol: 54.08 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Crystallized: 15% v/v PEG 3000, 200 mM magnesium chloride, 100 mM sodium cacodylate, pH 6.5; Crystals soaked in 15% PEG3000, 200 mM magnesium chloride, 100 mM sodium cacodylate, pH 6.5, and ...Details: Crystallized: 15% v/v PEG 3000, 200 mM magnesium chloride, 100 mM sodium cacodylate, pH 6.5; Crystals soaked in 15% PEG3000, 200 mM magnesium chloride, 100 mM sodium cacodylate, pH 6.5, and 750 uM FAD. Cryo: 15% v/v PEG3000, 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: Nov 8, 2019
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: 1.85→22.42 Å / Num. obs: 183821 / % possible obs: 98.5 % / Redundancy: 3.8 % / Rpim(I) all: 0.04 / Net I/σ(I): 6.4
Reflection shellResolution: 1.85→1.9 Å / Redundancy: 3.8 % / Num. unique obs: 18078 / Rpim(I) all: 0.485 / % possible all: 96.3

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Processing

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

7kav


Resolution: 1.854→22.42 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.42 / Phase error: 27.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2487 2005 1.09 %
Rwork0.1936 181771 -
obs0.1942 183776 98.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 112.29 Å2 / Biso mean: 29.2785 Å2 / Biso min: 6.04 Å2
Refinement stepCycle: final / Resolution: 1.854→22.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14099 0 331 2725 17155
Biso mean--35.06 37.68 -
Num. residues----1746
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01414613
X-RAY DIFFRACTIONf_angle_d1.16219802
X-RAY DIFFRACTIONf_dihedral_angle_d6.978710
X-RAY DIFFRACTIONf_chiral_restr0.0632162
X-RAY DIFFRACTIONf_plane_restr0.0082515
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.854-1.90020.4311410.37021266596
1.9002-1.95150.39831480.34081302599
1.9515-2.00890.3821350.30981297599
2.0089-2.07370.3181360.28041272597
2.0737-2.14780.29581490.23641303099
2.1478-2.23370.25331470.20241303099
2.2337-2.33530.24491370.18321308099
2.3353-2.45830.23861500.17671307499
2.4583-2.61210.24071460.1811309799
2.6121-2.81340.26881430.17751303199
2.8134-3.09580.23221390.1711277297
3.0958-3.54230.19711490.14491315499
3.5423-4.45720.17651380.13441305199
4.4572-22.420.23271470.18711306297

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