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- PDB-8wws: Crystal structure of cis-epoxysuccinate hydrolase from Klebsiella... -

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Basic information

Entry
Database: PDB / ID: 8wws
TitleCrystal structure of cis-epoxysuccinate hydrolase from Klebsiella oxytoca with L(+)-tartaric acid
Components(S)-2-haloacid dehalogenase
KeywordsHYDROLASE / cis-epoxysuccinate hydrolase
Function / homology
Function and homology information


hydrolase activity, acting on acid halide bonds, in C-halide compounds / metal ion binding
Similarity search - Function
L-2-Haloacid dehalogenase / : / HAD hydrolase, subfamily IA / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily
Similarity search - Domain/homology
CARBONATE ION / L(+)-TARTARIC ACID / Cis-epoxysuccinate hydrolase
Similarity search - Component
Biological speciesKlebsiella oxytoca (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsHan, Y. / Kong, X.D. / Li, J. / Xu, J.H.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2020YFA0907700 China
CitationJournal: Biochemistry / Year: 2024
Title: Structural Insights of a cis -Epoxysuccinate Hydrolase Facilitate the Development of Robust Biocatalysts for the Production of l-(+)-Tartrate.
Authors: Han, Y. / Luo, Y. / Ma, B.D. / Li, J. / Xu, J.H. / Kong, X.D.
History
DepositionOct 26, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 12, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 3, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: (S)-2-haloacid dehalogenase
B: (S)-2-haloacid dehalogenase
C: (S)-2-haloacid dehalogenase
D: (S)-2-haloacid dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,01710
Polymers123,4434
Non-polymers5746
Water12,304683
1
A: (S)-2-haloacid dehalogenase
hetero molecules

C: (S)-2-haloacid dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,9324
Polymers61,7222
Non-polymers2102
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1/2,y+1/2,-z-11
2
D: (S)-2-haloacid dehalogenase
hetero molecules

B: (S)-2-haloacid dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,0866
Polymers61,7222
Non-polymers3644
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_455x-1/2,-y+1/2,-z1
Unit cell
Length a, b, c (Å)114.616, 114.700, 86.310
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
(S)-2-haloacid dehalogenase


Mass: 30860.754 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella oxytoca (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: W8PFD2

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Non-polymers , 5 types, 689 molecules

#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: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 683 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.3 Å3/Da / Density % sol: 46.47 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium citrate, 0.1 M Bis-tris propane pH 6.5, 20-25% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.979183 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 16, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 1.79→47.75 Å / Num. obs: 105692 / % possible obs: 99.9 % / Redundancy: 7.7 % / CC1/2: 0.992 / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.052 / Rrim(I) all: 0.151 / Χ2: 0.84 / Net I/σ(I): 10.2
Reflection shellResolution: 1.79→1.83 Å / % possible obs: 99 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.504 / Num. measured all: 16214 / Num. unique obs: 3115 / CC1/2: 0.826 / Rpim(I) all: 0.243 / Rrim(I) all: 0.56 / Χ2: 0.34 / Net I/σ(I) obs: 2.2

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.79→44.08 Å / SU ML: 0 / Cross valid method: FREE R-VALUE / σ(F): 28.41 / Phase error: 23.23 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.219 5326 5.04 %
Rwork0.1826 --
obs0.1917 105692 99.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.79→44.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7394 0 38 683 8115
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097622
X-RAY DIFFRACTIONf_angle_d1.01510338
X-RAY DIFFRACTIONf_dihedral_angle_d7.0512763
X-RAY DIFFRACTIONf_chiral_restr0.0561129
X-RAY DIFFRACTIONf_plane_restr0.0081330
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.79-1.830.31282560.28374861X-RAY DIFFRACTION93
1.83-1.860.31932630.26985001X-RAY DIFFRACTION94
1.86-1.890.3152620.26534975X-RAY DIFFRACTION94
1.89-1.930.27532610.25134964X-RAY DIFFRACTION94
1.93-1.980.27092640.24745012X-RAY DIFFRACTION94
1.98-2.020.24492610.23254970X-RAY DIFFRACTION94
2.02-2.070.2522630.24374981X-RAY DIFFRACTION94
2.07-2.130.27022600.23144949X-RAY DIFFRACTION94
2.13-2.190.27852620.2374977X-RAY DIFFRACTION94
2.19-2.260.26672620.22934977X-RAY DIFFRACTION94
2.26-2.340.26742630.2294993X-RAY DIFFRACTION94
2.34-2.440.2572640.2295010X-RAY DIFFRACTION94
2.44-2.550.25972630.21855003X-RAY DIFFRACTION94
2.55-2.680.22282630.2085006X-RAY DIFFRACTION94
2.68-2.850.22522670.19695058X-RAY DIFFRACTION95
2.85-3.070.22682640.18535031X-RAY DIFFRACTION94
3.07-3.380.21772690.1735109X-RAY DIFFRACTION95
3.38-3.870.19532680.15035091X-RAY DIFFRACTION95
3.87-4.870.15772720.11965174X-RAY DIFFRACTION95
4.87-44.080.18892780.15985265X-RAY DIFFRACTION93

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