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- PDB-9iqj: Structure of oleate hydratase mutant L151V from Staphylococcus au... -

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Basic information

Entry
Database: PDB / ID: 9iqj
TitleStructure of oleate hydratase mutant L151V from Staphylococcus aureus in the complex with linoleic acid
ComponentsOleate hydratase
KeywordsLYASE / Oleate Hydratase
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
LINOLEIC ACID / DI(HYDROXYETHYL)ETHER / Myosin-cross-reactive antigen
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 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)204,89411
Polymers203,5363
Non-polymers1,3588
Water40,5522251
1
A: Oleate hydratase
B: Oleate hydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,5707
Polymers135,6912
Non-polymers8795
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7560 Å2
ΔGint0 kcal/mol
Surface area43140 Å2
MethodPISA
2
C: Oleate hydratase
hetero molecules

C: Oleate hydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,6488
Polymers135,6912
Non-polymers9576
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area7820 Å2
ΔGint-7 kcal/mol
Surface area42710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)189.355, 114.114, 119.113
Angle α, β, γ (deg.)90.000, 117.040, 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-1087-

HOH

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Components

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


Mass: 67845.484 Da / Num. of mol.: 3 / Mutation: L151V
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-EIC / LINOLEIC ACID / 9,12-LINOLEIC ACID


Mass: 280.445 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C18H32O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2251 / 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: 2.82 Å3/Da / Density % sol: 56.32 %
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: 1.64→37.82 Å / Num. obs: 274186 / % possible obs: 99.34 % / Redundancy: 6.8 % / Biso Wilson estimate: 14.7 Å2 / CC1/2: 0.993 / CC star: 0.998 / Rmerge(I) obs: 0.1108 / Rrim(I) all: 0.1201 / Net I/av σ(I): 14.58 / Net I/σ(I): 3.66
Reflection shellResolution: 1.64→1.69 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.4172 / Mean I/σ(I) obs: 3.66 / Num. unique obs: 26636 / CC1/2: 0.949 / CC star: 0.987 / Rrim(I) all: 0.4509 / % possible all: 96.94

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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: 1.64→37.82 Å / SU ML: 0.1338 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 17.3349
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.177 13552 0.74 %
Rwork0.1563 270938 -
obs0.1564 272947 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.84 Å2
Refinement stepCycle: LAST / Resolution: 1.64→37.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14093 0 94 2251 16438
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007214528
X-RAY DIFFRACTIONf_angle_d0.930419656
X-RAY DIFFRACTIONf_chiral_restr0.05832148
X-RAY DIFFRACTIONf_plane_restr0.00892522
X-RAY DIFFRACTIONf_dihedral_angle_d7.92991945
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.64-1.680.20751590.176818683X-RAY DIFFRACTION96.07
1.68-1.730.22041320.17519322X-RAY DIFFRACTION99.23
1.73-1.780.20721370.177319264X-RAY DIFFRACTION99.39
1.78-1.840.19031330.172719300X-RAY DIFFRACTION99.35
1.84-1.90.19871550.162919312X-RAY DIFFRACTION99.43
1.9-1.980.18861480.161119367X-RAY DIFFRACTION99.69
1.98-2.070.17581400.158219336X-RAY DIFFRACTION99.78
2.07-2.180.17461430.151719463X-RAY DIFFRACTION99.83
2.18-2.310.16081390.155219434X-RAY DIFFRACTION99.85
2.31-2.490.18491490.162619444X-RAY DIFFRACTION99.88
2.49-2.740.20421430.160319438X-RAY DIFFRACTION99.89
2.74-3.140.17681440.159219519X-RAY DIFFRACTION99.93
3.14-3.950.14011420.143319566X-RAY DIFFRACTION99.91
3.95-37.820.17351450.147419490X-RAY DIFFRACTION98.67

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