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- PDB-9iqi: Structure of oleate hydratase mutant - V135A/L212V from Staphyloc... -

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Basic information

Entry
Database: PDB / ID: 9iqi
TitleStructure of oleate hydratase mutant - V135A/L212V from Staphylococcus aureus in the complex with FAD
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 / FLAVIN-ADENINE DINUCLEOTIDE / Myosin-cross-reactive antigen
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.44 Å
AuthorsXue, S. / Feng, T.
Funding support China, 1items
OrganizationGrant numberCountry
Other government2021YFC2103702 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)205,0235
Polymers203,4523
Non-polymers1,5712
Water4,666259
1
A: Oleate hydratase
hetero molecules

A: Oleate hydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,2064
Polymers135,6352
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area7700 Å2
ΔGint-32 kcal/mol
Surface area42430 Å2
MethodPISA
2
B: Oleate hydratase
C: Oleate hydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,4203
Polymers135,6352
Non-polymers7861
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6140 Å2
ΔGint-23 kcal/mol
Surface area42400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)188.476, 109.809, 118.322
Angle α, β, γ (deg.)90.000, 116.610, 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
11A-788-

HOH

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Components

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


Mass: 67817.422 Da / Num. of mol.: 3 / Mutation: V135A,L212V
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: 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 259 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.69 Å3/Da / Density % sol: 54.28 %
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: 2.44→39.53 Å / Num. obs: 79192 / % possible obs: 97.95 % / Redundancy: 5.8 % / Biso Wilson estimate: 40.02 Å2 / CC1/2: 0.976 / CC star: 0.994 / Rmerge(I) obs: 0.1658 / Rrim(I) all: 0.1831 / Net I/σ(I): 12.77
Reflection shellResolution: 2.44→2.52 Å / Redundancy: 6 % / Rmerge(I) obs: 0.453 / Mean I/σ(I) obs: 2.72 / Num. unique obs: 7610 / CC1/2: 0.942 / CC star: 0.985 / % possible all: 94.65

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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: 2.44→39.53 Å / SU ML: 0.2705 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.3647
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2346 3915 4.98 %
Rwork0.2014 74706 -
obs0.2031 78621 97.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.67 Å2
Refinement stepCycle: LAST / Resolution: 2.44→39.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14192 0 106 259 14557
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002314635
X-RAY DIFFRACTIONf_angle_d0.515819854
X-RAY DIFFRACTIONf_chiral_restr0.04452165
X-RAY DIFFRACTIONf_plane_restr0.00442539
X-RAY DIFFRACTIONf_dihedral_angle_d6.55681912
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.44-2.470.34581090.28022295X-RAY DIFFRACTION84.26
2.47-2.50.29951290.26552623X-RAY DIFFRACTION97.14
2.5-2.530.27211260.25282688X-RAY DIFFRACTION97.51
2.53-2.570.28651270.25452637X-RAY DIFFRACTION97.02
2.57-2.60.33831340.26032657X-RAY DIFFRACTION97.28
2.6-2.640.32881410.26522591X-RAY DIFFRACTION96.88
2.64-2.680.29821500.25952676X-RAY DIFFRACTION97.52
2.68-2.730.30941360.25862637X-RAY DIFFRACTION97.4
2.73-2.770.35141300.26572668X-RAY DIFFRACTION97.83
2.77-2.820.31051230.24632679X-RAY DIFFRACTION98.07
2.82-2.880.30211440.24122695X-RAY DIFFRACTION97.8
2.88-2.940.27661320.25082651X-RAY DIFFRACTION98.37
2.94-30.35391230.2542699X-RAY DIFFRACTION98.36
3-3.070.27471380.25112676X-RAY DIFFRACTION98.49
3.07-3.150.27411270.24272685X-RAY DIFFRACTION98.25
3.15-3.230.26141640.24042672X-RAY DIFFRACTION98.64
3.23-3.330.28861580.23532675X-RAY DIFFRACTION98.78
3.33-3.440.25821500.21232675X-RAY DIFFRACTION98.81
3.44-3.560.23431300.20942690X-RAY DIFFRACTION98.91
3.56-3.70.23861420.19532716X-RAY DIFFRACTION99.1
3.7-3.870.21321310.17662722X-RAY DIFFRACTION99.23
3.87-4.070.17811560.17072720X-RAY DIFFRACTION99.21
4.07-4.330.17451560.16262686X-RAY DIFFRACTION99.27
4.33-4.660.19471630.15622697X-RAY DIFFRACTION99.51
4.66-5.130.18661810.16242689X-RAY DIFFRACTION99.41
5.13-5.870.19871330.17662740X-RAY DIFFRACTION99.52
5.87-7.390.25111450.1832762X-RAY DIFFRACTION99.38
7.39-39.530.17421370.15812705X-RAY DIFFRACTION95.79

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