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

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Basic information

Entry
Database: PDB / ID: 8wbq
TitleCrystal structure of cis-Epoxysuccinate Hydrolases RhCESH[L] mutant E212Q complexed with L-TA.
ComponentsEpoxide hydrolase
KeywordsHYDROLASE / cis-Epoxysuccinate Hydrolases / epoxide hydrolase / L(+)-tartaric acid
Function / homologyhydrolase activity, acting on halide bonds, in C-halide compounds / L-2-Haloacid dehalogenase / : / HAD hydrolase, subfamily IA / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily / L(+)-TARTARIC ACID / Epoxide hydrolase
Function and homology information
Biological speciesRhodococcus opacus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)59,0024
Polymers58,7022
Non-polymers3002
Water2,090116
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.643, 53.888, 61.959
Angle α, β, γ (deg.)67.070, 75.840, 75.970
Int Tables number1
Space group name H-MP1
Space group name HallP1

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Components

#1: Protein Epoxide hydrolase


Mass: 29350.924 Da / Num. of mol.: 2 / Mutation: E212Q
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-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.04 Å3/Da / Density % sol: 39.59 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2M sodium citrate tribasic, 0.2M potassium acetate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.978557 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 8, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978557 Å / Relative weight: 1
ReflectionResolution: 2.2→56.25 Å / Num. obs: 23063 / % possible obs: 98.2 % / Redundancy: 3.4 % / Biso Wilson estimate: 23.52 Å2 / CC1/2: 0.926 / Rmerge(I) obs: 0.245 / Rpim(I) all: 0.16 / Rrim(I) all: 0.294 / Χ2: 0.66 / Net I/σ(I): 5.8
Reflection shellResolution: 2.2→2.26 Å / % possible obs: 97.4 % / Redundancy: 2.9 % / Rmerge(I) obs: 1.221 / Num. measured all: 4933 / Num. unique obs: 1694 / CC1/2: 0.264 / Rpim(I) all: 0.875 / Rrim(I) all: 1.514 / Χ2: 0.56 / Net I/σ(I) obs: 3.3

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
DIALSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→56.25 Å / SU ML: 0.2493 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 26.148
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2395 1212 5.27 %
Rwork0.1825 21768 -
obs0.1855 22980 97.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.73 Å2
Refinement stepCycle: LAST / Resolution: 2.2→56.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3795 0 18 116 3929
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00413891
X-RAY DIFFRACTIONf_angle_d0.65675281
X-RAY DIFFRACTIONf_chiral_restr0.04587
X-RAY DIFFRACTIONf_plane_restr0.0055687
X-RAY DIFFRACTIONf_dihedral_angle_d12.2101541
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.290.31611370.23342338X-RAY DIFFRACTION95.86
2.29-2.390.27971340.21062431X-RAY DIFFRACTION96.98
2.39-2.520.29651280.21332392X-RAY DIFFRACTION97.22
2.52-2.680.25991430.19732433X-RAY DIFFRACTION97.8
2.68-2.880.29751330.19692409X-RAY DIFFRACTION98.03
2.88-3.170.2451450.19152428X-RAY DIFFRACTION98.39
3.17-3.630.23321320.17072444X-RAY DIFFRACTION98.66
3.63-4.580.21361230.15422464X-RAY DIFFRACTION99
4.58-56.250.18211370.16962429X-RAY DIFFRACTION98.28
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)
16.986772131743.28208948056-4.937288345184.32439028536-3.521537694327.18029889580.161417777329-0.1391362131990.1590676726250.511210548164-0.008942513179630.137783784866-0.467725913435-0.112967786022-0.1223860281090.213919678020.0160850978588-0.00814710705670.2040191475380.04197764263860.11498547550313.385311246616.416812415929.5203497556
26.648016186190.130898783194-2.893367742621.673944553420.3637544006452.8048362644-0.125668885191-0.4201446760690.22860523780.216978957197-0.401822569711-0.229090547389-0.2295043629910.4421969519990.3166168145670.2766770192470.0163496120553-0.0002404208634420.4895745629230.1125848563270.1576098851418.52198950298.037293939536.4544489851
32.865890143181.06337777195-2.690862746322.43250214149-0.2126945585532.86121642824-0.210516619377-0.0525710650569-0.466112441429-0.320868413573-0.152448508959-0.101724790350.3946622940240.2148917193740.3003048405160.2182694284850.03558800108810.04784525572820.3003020967840.1442703489390.22344425990818.82180828850.81879103170630.197899876
42.106239104461.97770318342-0.8530666783734.31169139456-0.9006407069941.47061506389-0.182826753755-0.009372507033970.00700010494741-0.1344111169050.1747036024350.0607338282635-0.0233548386236-0.341783081108-0.06650231117470.2019286743450.0411967165607-0.007150346094180.2971850891920.06313576254360.12396582087110.25431998913.388890498128.0222527988
52.301925723410.500497899043-0.8971750918663.31088258627-0.7794829533532.08383596029-0.09752273324730.0092195684805-0.2125216544250.0296405673671-0.091726726541-0.248555587888-0.2147077066970.3110328597360.1790859443030.20811765821-0.03291500712140.002293582533380.3109245940090.09175810861320.14739241941422.704070281414.861444717717.3222402917
67.35531613748-1.50017888351-2.696084584825.46921645152.961291016226.06005931384-0.214167278186-0.1915725339320.2054381928250.264084961198-0.18541693597-0.6106516081330.1983292967610.8254106500280.3947746530290.249433652406-0.11048593357-0.05332409886130.5564849713580.1069936252510.33519290857632.15895019120.895204663522.2593159031
73.61536020988-0.0678816983684-2.438382258171.066315762960.8317758135462.716772474930.110238260444-0.9271487170370.1566387840180.637746362889-0.303260597067-0.423770621753-0.4624065378290.7049991450290.138014757260.584959683424-0.189286917992-0.07732050164690.436586135013-0.01412968161570.22693248653524.753130641528.154794664729.8153279736
81.34353502267-0.3175548809440.2652617031990.3818349230170.1822789629390.393442842311-0.0380953170980.2129078528370.03680443390090.1263755456190.1735386467820.148183994844-0.125891584701-0.262102122276-0.1077867912930.2187580317030.02802275640190.01431879798770.4147337099280.1447125108230.23957479803212.561686228417.5978141159-4.01418874933
91.803188524640.665324752163-1.076706547494.12592496854-0.6758495418122.77891454527-0.04242376565040.301816979893-0.239985408635-0.219409356989-0.1913630947230.2033171487610.2512849365920.2929182439070.1444139054120.2351624713820.01752667249750.0689787334050.4786885324350.2030982604230.17380441615829.489903718416.5407217006-11.9291956521
102.11684756697-0.07866052219940.06983643395052.05835246435-0.4915771557363.04620625649-0.004698777254710.199530868161-0.0344865967331-0.120822863365-0.0225699727289-0.05443461018560.165093247599-0.08536865480350.0359174217720.194762740949-0.009230873322690.03205966818570.2647212467410.09049484090490.12468254113513.896917456911.37882727822.61424753654
111.869310636392.20527872246-2.127311322113.75853609304-3.502459261844.14060376396-0.1973781903450.5539565247070.118833648955-0.8441518390580.1543703028910.365647224830.298474924534-0.747712358765-0.05559290131520.333792775379-0.0505662466964-0.06375608351760.5596965833060.1284447983320.2237846930333.5619214075614.0605531011-7.39473139088
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 11 through 43 )AA11 - 431 - 33
22chain 'A' and (resid 44 through 67 )AA44 - 6734 - 57
33chain 'A' and (resid 68 through 88 )AA68 - 8858 - 78
44chain 'A' and (resid 89 through 125 )AA89 - 12579 - 115
55chain 'A' and (resid 126 through 177 )AA126 - 177116 - 167
66chain 'A' and (resid 178 through 200 )AA178 - 200168 - 190
77chain 'A' and (resid 201 through 246 )AA201 - 246191 - 236
88chain 'B' and (resid 3 through 43 )BC3 - 431 - 41
99chain 'B' and (resid 44 through 108 )BC44 - 10842 - 106
1010chain 'B' and (resid 109 through 207 )BC109 - 207107 - 205
1111chain 'B' and (resid 208 through 246 )BC208 - 246206 - 244

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