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- PDB-8wbn: Crystal structure of cis-Epoxysuccinate Hydrolases RhCESH[L] muta... -

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Basic information

Entry
Database: PDB / ID: 8wbn
TitleCrystal structure of cis-Epoxysuccinate Hydrolases RhCESH[L] mutant D193N
ComponentsEpoxide hydrolase
KeywordsHYDROLASE / cis-Epoxysuccinate Hydrolases / epoxide hydrolase / L(+)-tartaric acid
Function / homologyhydrolase activity, acting on acid halide bonds, in C-halide compounds / L-2-Haloacid dehalogenase / HAD hydrolase, subfamily IA / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily / Epoxide hydrolase
Function and homology information
Biological speciesRhodococcus opacus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsDong, S. / Xuan, J.S. / Feng, Y.G. / Cui, Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171203 China
CitationJournal: J.Biol.Chem. / Year: 2024
Title: Deciphering the stereo-specific catalytic mechanisms of cis-epoxysuccinate hydrolases producing L(+)-tartaric acid.
Authors: Dong, S. / Xuan, J. / Feng, Y. / Cui, Q.
History
DepositionSep 10, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 31, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2024Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)58,8944
Polymers58,7022
Non-polymers1922
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2190 Å2
ΔGint-45 kcal/mol
Surface area20040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.404, 58.552, 64.086
Angle α, β, γ (deg.)69.88, 73.55, 82.69
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Epoxide hydrolase /


Mass: 29350.920 Da / Num. of mol.: 2 / Mutation: D193N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus opacus (bacteria) / Gene: eph / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q1KLR5
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.5 Å3/Da / Density % sol: 50.74 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2M ammonium sulfate, 0.1M Bis-tris, pH6.5, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→48.55 Å / Num. obs: 17521 / % possible obs: 89.1 % / Redundancy: 1.9 % / CC1/2: 0.979 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.091 / Rrim(I) all: 0.129 / Χ2: 0.66 / Net I/σ(I): 4.3 / Num. measured all: 33094
Reflection shellResolution: 2.5→2.6 Å / % possible obs: 89.7 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.312 / Num. measured all: 3751 / Num. unique obs: 1990 / CC1/2: 0.824 / Rpim(I) all: 0.31 / Rrim(I) all: 0.44 / Χ2: 0.56 / Net I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→38.9 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 31.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2656 859 4.91 %
Rwork0.2106 --
obs0.2133 17508 89.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→38.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3716 0 10 13 3739
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023812
X-RAY DIFFRACTIONf_angle_d0.575185
X-RAY DIFFRACTIONf_dihedral_angle_d12.511373
X-RAY DIFFRACTIONf_chiral_restr0.039578
X-RAY DIFFRACTIONf_plane_restr0.005671
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.660.32671370.25842858X-RAY DIFFRACTION91
2.66-2.860.33091580.24542821X-RAY DIFFRACTION92
2.86-3.150.29321490.24272773X-RAY DIFFRACTION89
3.15-3.610.33031320.23632591X-RAY DIFFRACTION83
3.61-4.540.22161530.18412804X-RAY DIFFRACTION90
4.54-38.90.22681300.19062802X-RAY DIFFRACTION90
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.05940.4817-0.63160.7180.7411.1017-0.40830.77490.0997-0.65870.1534-0.13860.1121-0.41440.12710.4892-0.0901-0.00550.54520.00910.3756-3.951922.50625.7854
21.1176-0.533-0.01144.9218-2.39644.5209-0.20320.44450.0008-0.238-0.0237-0.16030.1032-0.14740.22410.4613-0.122-0.00650.7842-0.14020.47475.682815.110620.6577
38.21062.7225-2.87571.0526-0.85251.44950.12050.30720.5563-0.04810.11250.1198-0.29970.1628-0.25450.6378-0.18160.02450.702-0.07030.4317-1.112724.184627.9136
43.59341.19791.31760.35420.55382.44840.07440.2865-0.3455-0.20980.0628-0.01310.22480.0891-0.15240.5023-0.09490.0390.5387-0.06990.4076-7.17839.461233.9877
50.90631.37110.4975.44661.24043.2727-0.26190.560.0864-0.68570.17080.0465-0.3390.16560.10960.4549-0.1495-0.09040.7010.00880.3522-21.428711.851930.0043
62.65021.5638-0.29753.5566-2.17543.11620.4758-0.73360.14680.4989-0.21130.0791-0.31780.4702-0.26230.4324-0.10260.02720.634-0.12820.3488-6.822813.873164.4597
79.2759-0.3606-2.92163.1076-0.5734.24780.75-0.9212-0.04680.3446-0.8027-0.3131-0.71380.22280.12310.6218-0.2524-0.1610.73840.110.5187-0.22095.455370.354
84.54050.9909-2.23012.956-2.35544.1944-0.07310.0101-0.6343-0.0098-0.1983-0.38440.37120.15830.08880.5131-0.11740.00580.57010.00240.4613-5.5171-1.131365.5806
93.72270.25130.14316.4901-1.83764.80740.2-0.18120.4140.1146-0.34770.9221-0.0699-0.61170.2570.36690.0256-0.01150.5779-0.0560.4237-7.151624.359857.0067
102.64560.81260.45441.3758-0.36252.83790.4742-0.4814-0.12080.0556-0.35180.04610.00380.0476-0.11940.3826-0.1057-0.02810.58210.00580.343-2.330615.206751.053
112.9343.6154-2.88569.8803-5.41367.25080.42510.1254-0.59270.2475-0.667-0.88770.09321.20380.04850.4421-0.0898-0.01740.6693-0.06150.446911.247811.815950.8471
123.99472.3375-3.34363.7306-1.52756.24670.0369-0.4079-0.610.3977-0.5521-0.6207-0.13980.15880.32640.4398-0.1482-0.05110.8023-0.02690.46928.347520.820860.9269
133.84641.8022-1.64486.3494-3.55996.48590.3001-0.4246-0.20330.8235-0.0738-0.0862-0.83760.9637-0.18110.5963-0.21990.03870.7192-0.15930.57494.511730.46962.087
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 11 through 43 )
2X-RAY DIFFRACTION2chain 'A' and (resid 44 through 88 )
3X-RAY DIFFRACTION3chain 'A' and (resid 89 through 125 )
4X-RAY DIFFRACTION4chain 'A' and (resid 126 through 217 )
5X-RAY DIFFRACTION5chain 'A' and (resid 218 through 247 )
6X-RAY DIFFRACTION6chain 'B' and (resid 11 through 43 )
7X-RAY DIFFRACTION7chain 'B' and (resid 44 through 67 )
8X-RAY DIFFRACTION8chain 'B' and (resid 68 through 108 )
9X-RAY DIFFRACTION9chain 'B' and (resid 109 through 125 )
10X-RAY DIFFRACTION10chain 'B' and (resid 126 through 160 )
11X-RAY DIFFRACTION11chain 'B' and (resid 161 through 177 )
12X-RAY DIFFRACTION12chain 'B' and (resid 178 through 217 )
13X-RAY DIFFRACTION13chain 'B' and (resid 218 through 247 )

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