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- PDB-8jy1: Structure of Mangifera Indica Epoxide hydrolase 2 -

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Basic information

Entry
Database: PDB / ID: 8jy1
TitleStructure of Mangifera Indica Epoxide hydrolase 2
ComponentsEpoxide hydrolase-2
KeywordsPLANT PROTEIN / alpha-beta hydrolase epoxide hydrolase
Function / homologyepoxide hydrolase activity / Epoxide hydrolase-like / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold / Epoxide hydrolase-2
Function and homology information
Biological speciesMangifera indica (mango)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsBhoite, A.S. / Gupta, V.S. / Kulkarni, K.A.
Funding support India, 1items
OrganizationGrant numberCountry
Council of Scientific & Industrial Research (CSIR) India
CitationJournal: To Be Published
Title: Structure of Mangifera Indica Epoxide hydrolase 2
Authors: Bhoite, A.S. / Gupta, V.S. / Kulkarni, K.A.
History
DepositionJul 2, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Epoxide hydrolase-2
B: Epoxide hydrolase-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,6023
Polymers73,4072
Non-polymers1941
Water5,152286
1
A: Epoxide hydrolase-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8982
Polymers36,7041
Non-polymers1941
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Epoxide hydrolase-2


Theoretical massNumber of molelcules
Total (without water)36,7041
Polymers36,7041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.040, 99.040, 172.784
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Epoxide hydrolase-2


Mass: 36703.742 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mangifera indica (mango) / Gene: EH2 / Plasmid: pEXP5-CT/TOPO / Production host: Escherichia coli (E. coli) / Strain (production host): RIL / References: UniProt: A0A1U9ZCB5
#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C8H18O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.86 Å3/Da / Density % sol: 56.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1M trisodium citrate, 0.2M ammonium acetate, 30%w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→47.6 Å / Num. obs: 34442 / % possible obs: 100 % / Redundancy: 13 % / CC1/2: 0.999 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.029 / Rrim(I) all: 0.104 / Net I/σ(I): 21.3 / Num. measured all: 447486
Reflection shellResolution: 2.4→2.49 Å / % possible obs: 100 % / Redundancy: 13.2 % / Rmerge(I) obs: 0.907 / Num. measured all: 46837 / Num. unique obs: 3542 / CC1/2: 0.891 / Rpim(I) all: 0.258 / Rrim(I) all: 0.943 / Net I/σ(I) obs: 2.9

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→47.6 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2093 1654 4.82 %
Rwork0.1759 --
obs0.1776 34350 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→47.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4334 0 13 286 4633
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024496
X-RAY DIFFRACTIONf_angle_d0.4596118
X-RAY DIFFRACTIONf_dihedral_angle_d10.8961584
X-RAY DIFFRACTIONf_chiral_restr0.045647
X-RAY DIFFRACTIONf_plane_restr0.004784
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.470.25961350.22432668X-RAY DIFFRACTION100
2.47-2.550.26381270.21852687X-RAY DIFFRACTION100
2.55-2.640.2641530.20922645X-RAY DIFFRACTION100
2.64-2.750.28771330.20062699X-RAY DIFFRACTION100
2.75-2.870.21011560.1872652X-RAY DIFFRACTION100
2.87-3.020.18291300.17822704X-RAY DIFFRACTION100
3.02-3.210.20991310.17122714X-RAY DIFFRACTION100
3.21-3.460.19551380.16192705X-RAY DIFFRACTION100
3.46-3.810.18491380.15682730X-RAY DIFFRACTION100
3.81-4.360.17441390.14582743X-RAY DIFFRACTION100
4.36-5.490.17961160.15422823X-RAY DIFFRACTION100
5.49-47.60.22771580.2022926X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 16.86 Å / Origin y: 40.1446 Å / Origin z: 59.7091 Å
111213212223313233
T0.1041 Å2-0.0213 Å2-0.0071 Å2-0.033 Å20.0303 Å2--0.1311 Å2
L0.8212 °2-0.4764 °20.5659 °2-1.0002 °2-1.3185 °2--2.0364 °2
S0.0641 Å °0.1503 Å °-0.0254 Å °-0.085 Å °-0.027 Å °0.0511 Å °0.078 Å °0.2272 Å °0.0433 Å °
Refinement TLS groupSelection details: all

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