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- PDB-9iqa: structure of the oleate hydratase V206L-mutant from Staphylococcu... -

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Basic information

Entry
Database: PDB / ID: 9iqa
Titlestructure of the oleate hydratase V206L-mutant from Staphylococcus aureus
ComponentsOleate hydratase
KeywordsLYASE / oleate hydratase
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: 2.09 Å
AuthorsXue, S. / Feng, T.
Funding support China, 1items
OrganizationGrant numberCountry
Other government China
CitationJournal: To Be Published
Title: Cooperative Evolution of Oleate Hydratase via Combinatorial Distal Site Mutations
Authors: Xue, S. / Feng, T.
History
DepositionJul 12, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release

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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


Theoretical massNumber of molelcules
Total (without water)203,6213
Polymers203,6213
Non-polymers00
Water27,3651519
1
A: Oleate hydratase
B: Oleate hydratase


Theoretical massNumber of molelcules
Total (without water)135,7472
Polymers135,7472
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4760 Å2
ΔGint-12 kcal/mol
Surface area44010 Å2
MethodPISA
2
C: Oleate hydratase

C: Oleate hydratase


Theoretical massNumber of molelcules
Total (without water)135,7472
Polymers135,7472
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area4770 Å2
ΔGint-13 kcal/mol
Surface area44160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)189.181, 113.062, 118.973
Angle α, β, γ (deg.)90.000, 117.120, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11C-859-

HOH

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Components

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


Mass: 67873.539 Da / Num. of mol.: 3 / Mutation: V206L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria)
Gene: EP54_06595, EQ90_12415, GO814_02765, GO942_14045, GZ163_10760, HMPREF3211_02399
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0D6GJV1, oleate hydratase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1519 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.82 Å3/Da / Density % sol: 56.43 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Ammooium citrate tribasic pH 7.0, 15 % w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17B1 / Wavelength: 0.9793 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jan 9, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.09→42.1 Å / Num. obs: 128561 / % possible obs: 96.3 % / Redundancy: 3.9 % / Biso Wilson estimate: 24.51 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.11 / Rrim(I) all: 0.13 / Net I/σ(I): 11.03
Reflection shellResolution: 2.09→2.17 Å / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 4.39 / Num. unique obs: 10524 / CC1/2: 0.764 / Rpim(I) all: 0.32 / Rrim(I) all: 0.66

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-3000v721data reduction
HKL-3000v721data scaling
PHENIX1.20.1_4487phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7KAW

7kaw


Resolution: 2.09→42.1 Å / SU ML: 0.1723 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.7066
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1878 6420 5.09 %
Rwork0.1617 119696 -
obs0.1631 126116 96.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.74 Å2
Refinement stepCycle: LAST / Resolution: 2.09→42.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14117 0 0 1519 15636
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002214443
X-RAY DIFFRACTIONf_angle_d0.507219568
X-RAY DIFFRACTIONf_chiral_restr0.04312145
X-RAY DIFFRACTIONf_plane_restr0.00362510
X-RAY DIFFRACTIONf_dihedral_angle_d5.41731885
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.09-2.120.25041430.19512552X-RAY DIFFRACTION61.53
2.12-2.140.24181910.18783658X-RAY DIFFRACTION88.77
2.14-2.170.22842030.18723777X-RAY DIFFRACTION91.54
2.17-2.20.22672060.18143842X-RAY DIFFRACTION93.4
2.2-2.230.21491970.18163842X-RAY DIFFRACTION92.47
2.23-2.260.24362120.19733881X-RAY DIFFRACTION94.27
2.26-2.290.2142290.18774000X-RAY DIFFRACTION97
2.29-2.320.22032060.17183982X-RAY DIFFRACTION97.51
2.32-2.360.21772000.17874096X-RAY DIFFRACTION98.17
2.36-2.40.2252200.18294059X-RAY DIFFRACTION97.98
2.4-2.440.22492130.17844042X-RAY DIFFRACTION97.93
2.44-2.480.21782070.18014045X-RAY DIFFRACTION97.68
2.48-2.530.21172170.17854045X-RAY DIFFRACTION97.84
2.53-2.580.22992030.18074093X-RAY DIFFRACTION98.42
2.58-2.640.22942140.17474062X-RAY DIFFRACTION98.57
2.64-2.70.19992310.17574060X-RAY DIFFRACTION98.49
2.7-2.770.21392030.16994088X-RAY DIFFRACTION98.78
2.77-2.840.20061970.17074068X-RAY DIFFRACTION98.66
2.84-2.930.18662280.16924112X-RAY DIFFRACTION99.13
2.93-3.020.19032350.17254092X-RAY DIFFRACTION99.22
3.02-3.130.19422320.17534091X-RAY DIFFRACTION99.13
3.13-3.250.20322250.16994129X-RAY DIFFRACTION99.41
3.25-3.40.19242140.1634124X-RAY DIFFRACTION99.5
3.4-3.580.16412320.15034112X-RAY DIFFRACTION99.43
3.58-3.80.16592120.14214160X-RAY DIFFRACTION99.39
3.8-4.10.16152500.13324095X-RAY DIFFRACTION99.54
4.1-4.510.13872450.12924111X-RAY DIFFRACTION99.63
4.51-5.160.14942110.13684173X-RAY DIFFRACTION99.5
5.16-6.50.18582150.16124164X-RAY DIFFRACTION99.32
6.5-42.10.16382290.15694141X-RAY DIFFRACTION97.28

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