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- PDB-8hgu: Epoxide hydrolase from Bosea sp. PAMC 26642 -

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Basic information

Entry
Database: PDB / ID: 8hgu
TitleEpoxide hydrolase from Bosea sp. PAMC 26642
ComponentsAlpha/beta hydrolase
KeywordsHYDROLASE
Biological speciesBosea sp. PAMC 26642 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsLee, M.J. / Hwang, J. / Do, H. / Lee, J.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)PM22030 Korea, Republic Of
CitationJournal: Int.J.Biol.Macromol. / Year: 2024
Title: Structural insights into the distinct substrate preferences of two bacterial epoxide hydrolases.
Authors: Hwang, J. / Lee, M.J. / Lee, S.G. / Do, H. / Lee, J.H.
History
DepositionNov 15, 2022Deposition site: PDBJ / Processing site: RCSB
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha/beta hydrolase
B: Alpha/beta hydrolase
C: Alpha/beta hydrolase
D: Alpha/beta hydrolase


Theoretical massNumber of molelcules
Total (without water)133,0254
Polymers133,0254
Non-polymers00
Water11,602644
1
A: Alpha/beta hydrolase
B: Alpha/beta hydrolase


Theoretical massNumber of molelcules
Total (without water)66,5132
Polymers66,5132
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2380 Å2
ΔGint-20 kcal/mol
Surface area21200 Å2
MethodPISA
2
C: Alpha/beta hydrolase

D: Alpha/beta hydrolase


Theoretical massNumber of molelcules
Total (without water)66,5132
Polymers66,5132
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area2350 Å2
ΔGint-21 kcal/mol
Surface area21360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.537, 84.913, 98.235
Angle α, β, γ (deg.)90.000, 100.910, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Alpha/beta hydrolase


Mass: 33256.266 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bosea sp. PAMC 26642 (bacteria) / Gene: AXW83_17570 / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 644 / 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: 2.69 Å3/Da / Density % sol: 54.36 %
Crystal growTemperature: 296.15 K / Method: vapor diffusion, sitting drop
Details: 1 M Ammonium formate, 0.1 M Sodium acetate pH 5.0, 8 % w/v PGA (Na+ form, LM)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 27, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.94→50 Å / Num. obs: 101095 / % possible obs: 97.6 % / Redundancy: 4.4 % / Biso Wilson estimate: 19.34 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 29.96
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 4.23 / Num. unique obs: 4384 / % possible all: 85.3

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Processing

Software
NameVersionClassification
REFMAC1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EHY

1ehy


Resolution: 1.94→30.2 Å / SU ML: 0.1886 / Cross valid method: FREE R-VALUE / σ(F): 1.45 / Phase error: 19.951
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2078 5042 4.99 %
Rwork0.1721 96026 -
obs0.1739 101068 96.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.8 Å2
Refinement stepCycle: LAST / Resolution: 1.94→30.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9326 0 0 644 9970
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0159646
X-RAY DIFFRACTIONf_angle_d1.747613156
X-RAY DIFFRACTIONf_chiral_restr0.09081351
X-RAY DIFFRACTIONf_plane_restr0.01111743
X-RAY DIFFRACTIONf_dihedral_angle_d14.14983322
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.94-1.960.29581210.26022128X-RAY DIFFRACTION65.36
1.96-1.990.28231490.24122998X-RAY DIFFRACTION91.03
1.99-2.010.25091640.21523124X-RAY DIFFRACTION95.69
2.01-2.040.2021700.2023173X-RAY DIFFRACTION96.12
2.04-2.060.23061600.21353144X-RAY DIFFRACTION95.99
2.06-2.090.23721940.19853180X-RAY DIFFRACTION96.62
2.09-2.120.22281500.19633201X-RAY DIFFRACTION97.81
2.12-2.150.23211390.19283231X-RAY DIFFRACTION97.82
2.15-2.190.21411670.18253250X-RAY DIFFRACTION97.85
2.19-2.220.23421630.17883213X-RAY DIFFRACTION97.91
2.22-2.260.21461720.18043213X-RAY DIFFRACTION98.2
2.26-2.30.24681680.18243278X-RAY DIFFRACTION98.04
2.3-2.350.21651820.18413187X-RAY DIFFRACTION98.34
2.35-2.390.21611730.17413225X-RAY DIFFRACTION97.93
2.39-2.450.18891530.17453236X-RAY DIFFRACTION98.06
2.45-2.50.20621690.1693243X-RAY DIFFRACTION98.13
2.5-2.570.21491720.16253235X-RAY DIFFRACTION98.87
2.57-2.640.25371780.17793239X-RAY DIFFRACTION98.44
2.64-2.710.22891820.17913248X-RAY DIFFRACTION98.65
2.71-2.80.21381790.18023248X-RAY DIFFRACTION99.02
2.8-2.90.24261870.18733280X-RAY DIFFRACTION99.06
2.9-3.020.26081680.19443282X-RAY DIFFRACTION99.37
3.02-3.150.28051980.19433246X-RAY DIFFRACTION99.25
3.15-3.320.2251380.18393322X-RAY DIFFRACTION99.31
3.32-3.530.20642030.17473263X-RAY DIFFRACTION99.17
3.53-3.80.17041860.15283293X-RAY DIFFRACTION99.71
3.8-4.180.1541640.13993313X-RAY DIFFRACTION99.6
4.18-4.780.15261610.13023325X-RAY DIFFRACTION99.8
4.78-6.020.14261640.14183362X-RAY DIFFRACTION99.83

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