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- PDB-7kaw: Crystal structure of OhyA-PEG400-FAD complex from Staphylococcus ... -

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Basic information

Entry
Database: PDB / ID: 7kaw
TitleCrystal structure of OhyA-PEG400-FAD complex from Staphylococcus aureus
ComponentsOleate hydratase
KeywordsOXIDOREDUCTASE / Oleate hydratase / OhyA / SaOhyA / Complex / PEG400 / FAD
Function / homologyoleate hydratase / oleate hydratase activity / Oleate hydratase / MCRA family / FAD binding / fatty acid metabolic process / FAD/NAD(P)-binding domain superfamily / FLAVIN-ADENINE DINUCLEOTIDE / Myosin-cross-reactive antigen
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.105 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
C: Oleate hydratase
B: Oleate hydratase
A: Oleate hydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,46512
Polymers209,6783
Non-polymers2,7869
Water31,3641741
1
C: Oleate hydratase
hetero molecules

C: Oleate hydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,1058
Polymers139,7852
Non-polymers2,3206
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area9840 Å2
ΔGint-26 kcal/mol
Surface area41110 Å2
MethodPISA
2
B: Oleate hydratase
A: Oleate hydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,4128
Polymers139,7852
Non-polymers1,6266
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8300 Å2
ΔGint-15 kcal/mol
Surface area41850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)188.080, 112.919, 119.059
Angle α, β, γ (deg.)90.000, 116.970, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-933-

HOH

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Components

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


Mass: 69892.719 Da / Num. of mol.: 3
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-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H26O7 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1741 / 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: 2.69 Å3/Da / Density % sol: 54.22 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: Crystallized in: 20% PEG 400, 100 mM calcium acetate, 100 mM MES, pH 6.0; Soaked in same buffer containing 750 uM FAD. Cryo: 20% PEG 400, 100 mM calcium acetate, 100 mM MES, pH 6.0, 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, 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: 2.1→23 Å / Num. obs: 126745 / % possible obs: 98.9 % / Redundancy: 7.3 % / Rpim(I) all: 0.023 / Net I/σ(I): 7.8
Reflection shellResolution: 2.1→2.17 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 12711 / Rpim(I) all: 0.135 / % possible all: 99.4

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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: 2.105→22.999 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.49 / Phase error: 25.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.232 2004 1.58 %
Rwork0.1894 124641 -
obs0.19 126645 98.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 84.07 Å2 / Biso mean: 35.8638 Å2 / Biso min: 15.93 Å2
Refinement stepCycle: final / Resolution: 2.105→22.999 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14167 0 203 1741 16111
Biso mean--35.41 42.75 -
Num. residues----1757
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00714703
X-RAY DIFFRACTIONf_angle_d0.81719917
X-RAY DIFFRACTIONf_dihedral_angle_d7.2568761
X-RAY DIFFRACTIONf_chiral_restr0.0512171
X-RAY DIFFRACTIONf_plane_restr0.0052531
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.105-2.15740.33011400.2926893899
2.1574-2.21560.29751520.2718889199
2.2156-2.28080.30351430.2546891099
2.2808-2.35430.3221390.2403889599
2.3543-2.43840.30621420.2293890999
2.4384-2.53590.26731460.2211887099
2.5359-2.65120.29061390.2019884098
2.6512-2.79070.22091480.1897879798
2.7907-2.96520.25921320.1942876097
2.9652-3.19360.23591420.1807894099
3.1936-3.5140.20541510.16039012100
3.514-4.02010.18071390.15458992100
4.0201-5.0560.19571460.1488897099
5.056-22.9990.20581450.1924891797

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