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- PDB-8zp6: Crystal structure of Epoxide hydrolase MdEH (Mycobacterium dioxan... -

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Basic information

Entry
Database: PDB / ID: 8zp6
TitleCrystal structure of Epoxide hydrolase MdEH (Mycobacterium dioxanotrophicus)
ComponentsAB hydrolase-1 domain-containing protein
KeywordsHYDROLASE / Epoxide hydrolase
Function / homologyEpoxide hydrolase-like / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold / hydrolase activity / AB hydrolase-1 domain-containing protein
Function and homology information
Biological speciesMycobacterium dioxanotrophicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.10007468686 Å
AuthorsZhou, Y. / Lan, D.M. / Wang, Y.H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To be published
Title: Crystal structure of Epoxide hydrolase MdEH (Mycobacterium dioxanotrophicus)
Authors: Zhou, Y. / Lan, D.M. / Wang, Y.H.
History
DepositionMay 29, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 4, 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: AB hydrolase-1 domain-containing protein


Theoretical massNumber of molelcules
Total (without water)33,8331
Polymers33,8331
Non-polymers00
Water6,666370
1
A: AB hydrolase-1 domain-containing protein
x 6


Theoretical massNumber of molelcules
Total (without water)202,9996
Polymers202,9996
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
crystal symmetry operation10_455y-1/3,x+1/3,-z+1/31
crystal symmetry operation11_565x-y+2/3,-y+4/3,-z+1/31
crystal symmetry operation12_555-x+2/3,-x+y+1/3,-z+1/31
Buried area9710 Å2
ΔGint-93 kcal/mol
Surface area58930 Å2
MethodPISA
2
A: AB hydrolase-1 domain-containing protein

A: AB hydrolase-1 domain-containing protein


Theoretical massNumber of molelcules
Total (without water)67,6662
Polymers67,6662
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_455y-1/3,x+1/3,-z+1/31
Buried area2160 Å2
ΔGint-24 kcal/mol
Surface area20720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)179.29, 179.29, 151.35
Angle α, β, γ (deg.)90.0, 90.0, 120.0
Int Tables number155
Space group name H-MH32
Space group name HallR32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3
Components on special symmetry positions
IDModelComponents
11A-429-

HOH

21A-582-

HOH

31A-652-

HOH

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Components

#1: Protein AB hydrolase-1 domain-containing protein / Epoxide hydrolase


Mass: 33833.113 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium dioxanotrophicus (bacteria)
Gene: BTO20_37290 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1Y0CH10
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 370 / 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

Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 8
Details: Polyethylene glycol 3350, Ammonium sulfate, Bis-Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 5, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.01→31.8 Å / Num. obs: 61853 / % possible obs: 100 % / Redundancy: 19.5 % / CC1/2: 0.92 / Net I/σ(I): 3.6
Reflection shellResolution: 2.01→2.06 Å / Num. unique obs: 61853 / CC1/2: 0.684

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Processing

Software
NameVersionClassification
PHENIX1.9_1692+SVNrefinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.10007468686→30.4202143907 Å / SU ML: 0.253658741634 / Cross valid method: FREE R-VALUE / σ(F): 1.33645361864 / Phase error: 27.0605106408
RfactorNum. reflection% reflection
Rfree0.257517101071 1755 3.23269907348 %
Rwork0.239857369321 52534 -
obs0.240429651677 54289 99.9337321675 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.0799902565 Å2
Refinement stepCycle: LAST / Resolution: 2.10007468686→30.4202143907 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2379 0 0 370 2749
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00640378452172459
X-RAY DIFFRACTIONf_angle_d1.008049859183357
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1001-2.15680.2996833389771330.2723617826773988X-RAY DIFFRACTION99.6855345912
2.1568-2.22030.3077404549051350.2653163645744007X-RAY DIFFRACTION99.9758629013
2.2203-2.29190.2950167818661330.2757765086884014X-RAY DIFFRACTION99.9758919961
2.2919-2.37380.2855808725421340.2728559953744011X-RAY DIFFRACTION100
2.3738-2.46880.2953624762021340.2665494136154022X-RAY DIFFRACTION99.7120921305
2.4688-2.58110.2650313128381340.2685250379384024X-RAY DIFFRACTION99.9759557586
2.5811-2.71710.2925212641671340.2727473289924008X-RAY DIFFRACTION100
2.7171-2.88720.3008885760031360.261160032414052X-RAY DIFFRACTION100
2.8872-3.110.2442205323011350.2488357646874040X-RAY DIFFRACTION100
3.11-3.42260.2682886045021350.2312078960424026X-RAY DIFFRACTION100
3.4226-3.91690.2322148756481350.2151886820094066X-RAY DIFFRACTION100
3.9169-4.93150.2251636946761370.2086002373524089X-RAY DIFFRACTION100

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