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- PDB-5z70: Crystal structure of oleate hydratase from Stenotrophomonas sp. K... -

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Basic information

Entry
Database: PDB / ID: 5z70
TitleCrystal structure of oleate hydratase from Stenotrophomonas sp. KCTC 12332
ComponentsOleate hydratase
KeywordsHYDROLASE / oleate hydratase
Function / homologyoleate hydratase activity / Oleate hydratase / MCRA family / FAD binding / fatty acid metabolic process / FAD/NAD(P)-binding domain superfamily / Oleate hydratase
Function and homology information
Biological speciesStenotrophomonas sp. KCTC 12332 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.91 Å
AuthorsPark, A.K.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2018
Title: Crystal structure of oleate hydratase from Stenotrophomonas sp. KCTC 12332 reveals conformational plasticity surrounding the FAD binding site.
Authors: Park, A.K. / Lee, G.H. / Kim, D.W. / Jang, E.H. / Kwon, H.T. / Chi, Y.M.
History
DepositionJan 26, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2019Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.2Nov 22, 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
A: Oleate hydratase
B: Oleate hydratase


Theoretical massNumber of molelcules
Total (without water)135,2672
Polymers135,2672
Non-polymers00
Water1267
1
A: Oleate hydratase

A: Oleate hydratase


Theoretical massNumber of molelcules
Total (without water)135,2672
Polymers135,2672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area1690 Å2
ΔGint-13 kcal/mol
Surface area44330 Å2
MethodPISA
2
B: Oleate hydratase

B: Oleate hydratase


Theoretical massNumber of molelcules
Total (without water)135,2672
Polymers135,2672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area1470 Å2
ΔGint-11 kcal/mol
Surface area43870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.061, 235.252, 176.372
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Oleate hydratase


Mass: 67633.391 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Stenotrophomonas sp. KCTC 12332 (bacteria)
Gene: AXG53_12705 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A126NKL7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O

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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: 2.21 Å3/Da / Density % sol: 44.32 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: Bis-Tris propane, Potassium thiocyanate, PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 28812 / % possible obs: 99.8 % / Redundancy: 14.4 % / Biso Wilson estimate: 75.04 Å2 / Rmerge(I) obs: 0.257 / Rpim(I) all: 0.071 / Rrim(I) all: 0.266 / Χ2: 3.856 / Net I/σ(I): 5.9 / Num. measured all: 415860
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.9-2.95143.15114380.5190.8693.271.311100
2.95-314.32.62113970.5770.7152.7171.335100
3-3.0614.52.01914260.7240.5472.0931.359100
3.06-3.1214.61.73414320.780.4681.7961.399100
3.12-3.1914.81.44814190.8320.3891.4991.398100
3.19-3.2714.81.07614190.8910.2881.1141.569100
3.27-3.3514.80.8614190.9210.2310.8911.497100
3.35-3.4414.70.6114360.9580.1640.6321.603100
3.44-3.5414.80.51214060.9580.1380.531.725100
3.54-3.6514.80.39214570.9820.1060.4071.946100
3.65-3.7814.70.32614170.9840.0880.3382.14100
3.78-3.9414.70.2814280.9840.0760.292.415100
3.94-4.1114.70.22814430.990.0610.2372.844100
4.11-4.3314.60.18814470.9920.0510.1953.487100
4.33-4.614.60.16414310.9930.0440.174.497100
4.6-4.9614.60.16414480.9920.0450.175.277100
4.96-5.4614.40.16314660.990.0450.1696.048100
5.46-6.2414.20.15314850.9880.0420.1587.411100
6.24-7.8613.70.11314820.9940.0320.1188.76399.9
7.86-5012.40.10715160.9880.0330.11221.01196.1

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-2000data reduction
SCALEPACKdata scaling
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4UIR

4uir


Resolution: 2.91→35.827 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 32.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.29 1514 5.26 %RANDOM
Rwork0.2265 27247 --
obs0.2299 28761 99.51 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 142.87 Å2 / Biso mean: 71.758 Å2 / Biso min: 26.99 Å2
Refinement stepCycle: final / Resolution: 2.91→35.827 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8599 0 0 7 8606
Biso mean---52.25 -
Num. residues----1081
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0048807
X-RAY DIFFRACTIONf_angle_d0.85211957
X-RAY DIFFRACTIONf_chiral_restr0.0461306
X-RAY DIFFRACTIONf_plane_restr0.0071544
X-RAY DIFFRACTIONf_dihedral_angle_d18.1523212
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9097-3.00360.37971450.322372251797
3.0036-3.11090.39631320.302724522584100
3.1109-3.23540.34591130.295724662579100
3.2354-3.38250.41481340.271924592593100
3.3825-3.56070.31461380.247424652603100
3.5607-3.78350.34091370.236624602597100
3.7835-4.07530.29071610.222524672628100
4.0753-4.48470.26061280.194824902618100
4.4847-5.1320.25071330.200525232656100
5.132-6.45960.29311400.225225212661100
6.4596-35.82980.23811530.2042572272598

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