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- PDB-8wbr: Crystal structure of cis-Epoxysuccinate Hydrolases KlCESH[L] -

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Basic information

Entry
Database: PDB / ID: 8wbr
TitleCrystal structure of cis-Epoxysuccinate Hydrolases KlCESH[L]
Components(S)-2-haloacid dehalogenase(S)-2-haloacid dehalogenase
KeywordsHYDROLASE / cis-Epoxysuccinate Hydrolases / epoxide hydrolase / L(+)-tartaric acid
Function / homology(S)-2-haloacid dehalogenase / (S)-2-haloacid dehalogenase activity / L-2-Haloacid dehalogenase / HAD hydrolase, subfamily IA / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily / metal ion binding / (S)-2-haloacid dehalogenase
Function and homology information
Biological speciesKlebsiella sp. BK-58 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 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: (S)-2-haloacid dehalogenase
B: (S)-2-haloacid dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8623
Polymers54,8222
Non-polymers401
Water4,396244
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1730 Å2
ΔGint-17 kcal/mol
Surface area20480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.300, 84.749, 92.851
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 27411.088 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella sp. BK-58 (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: W8PFD2
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 244 / 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: 2.38 Å3/Da / Density % sol: 48.3 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.2M Potassium formate, 20% 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 9M / Detector: PIXEL / Date: Jun 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.02→38.55 Å / Num. obs: 34818 / % possible obs: 99.5 % / Redundancy: 6.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.037 / Rrim(I) all: 0.092 / Χ2: 0.94 / Net I/σ(I): 11.3 / Num. measured all: 216051
Reflection shellResolution: 2.02→2.07 Å / % possible obs: 99 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.954 / Num. measured all: 13830 / Num. unique obs: 2517 / CC1/2: 0.817 / Rpim(I) all: 0.475 / Rrim(I) all: 1.071 / Χ2: 0.91 / Net I/σ(I) obs: 2.4

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.02→30.872 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.235 1655 4.89 %
Rwork0.2064 --
obs0.2078 33877 96.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.02→30.872 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3718 0 1 244 3963
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023805
X-RAY DIFFRACTIONf_angle_d0.5485164
X-RAY DIFFRACTIONf_dihedral_angle_d5.8862263
X-RAY DIFFRACTIONf_chiral_restr0.038568
X-RAY DIFFRACTIONf_plane_restr0.003662
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.02-2.07950.39611240.33742530X-RAY DIFFRACTION93
2.0795-2.14660.30881610.27162683X-RAY DIFFRACTION99
2.1466-2.22330.36771360.30642530X-RAY DIFFRACTION93
2.2233-2.31230.41371090.37512227X-RAY DIFFRACTION82
2.3123-2.41750.25871370.22612757X-RAY DIFFRACTION100
2.4175-2.54490.26971320.22122730X-RAY DIFFRACTION99
2.5449-2.70420.24511460.2342740X-RAY DIFFRACTION100
2.7042-2.91290.2751200.22232788X-RAY DIFFRACTION100
2.9129-3.20570.25381650.21812732X-RAY DIFFRACTION100
3.2057-3.66890.2161290.20932774X-RAY DIFFRACTION99
3.6689-4.620.17171360.16662808X-RAY DIFFRACTION99
4.62-30.870.19841600.1592923X-RAY DIFFRACTION99
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)
19.15033.40616.88543.78283.36278.960.04320.7635-0.1775-0.19310.0255-0.1109-0.12250.5782-0.08680.25540.02040.01320.2816-0.00830.25161.96775.223912.083
27.8469-1.52552.77696.1139-1.55581.5497-0.0344-1.07980.62720.5568-0.0175-0.3118-0.00960.22550.12530.3237-0.0228-0.02240.5197-0.030.304118.33830.794433.0308
38.03775.04335.60254.90096.10417.3576-0.16140.9619-0.2305-1.12290.36550.0627-1.09050.905-0.17020.42950.0423-0.00490.437-0.04540.3619.6066-6.734418.7217
45.93772.02812.69496.34911.83177.48420.41020.9387-0.8847-0.2030.02380.07520.7420.3931-0.45450.32160.0874-0.03720.3773-0.04060.427915.4522-14.040220.0165
54.6854-3.82742.32874.7321-1.73642.5241-0.0538-0.39680.00790.38630.1216-0.17520.0401-0.0472-0.03160.2862-0.0408-0.01780.37530.0090.27589.8781-0.555526.9247
62.1663-0.26880.5662.1673-0.48212.12620.04020.1834-0.1922-0.2248-0.1226-0.0360.0626-0.03860.04790.24620.0106-0.0130.2763-0.02120.3429-0.7284-1.33810.9328
73.71290.93871.67573.80792.0577.1999-0.10190.4877-0.122-0.27730.089-0.3627-0.00950.51460.05720.28650.02720.05670.31060.0360.296911.38989.04716.6066
81.44140.53451.1118.71881.1785.4881-0.0944-0.42560.72740.2303-0.28350.5426-1.1319-0.96840.38140.38750.09710.02180.3874-0.00810.292-1.923617.907811.6079
97.1551-2.08346.47475.1644-2.55029.17620.3593-0.1687-0.60650.14460.08930.35720.1951-0.4138-0.44360.2862-0.01150.07370.30430.03190.4806-16.997-9.353223.1558
101.9947-1.46122.24736.5677-3.39034.318-0.92970.20320.4732-1.13030.80530.9422-1.1314-2.41410.07690.73440.0364-0.19520.9848-0.04370.7611-35.1375-0.56785.6232
116.67451.5439-2.04698.63331.88857.7911-0.13560.5871-0.093-0.3479-0.15780.91311.8232-0.62370.16060.8521-0.086-0.0990.7187-0.10480.6386-26.0432-10.84470.1356
122.73160.59850.46251.6261-0.83282.192-0.05680.1064-0.1465-0.0722-0.01420.00170.0885-0.04010.08140.20180.0090.00350.2406-0.05140.3784-13.443-8.721319.9404
136.6819-2.4321.94491.7232-1.31383.64820.0782-0.5536-0.6377-0.02590.04970.38850.097-0.3498-0.11290.2804-0.03220.03690.3161-0.00230.497-23.7607-15.142227.54
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 41 through 55 )
2X-RAY DIFFRACTION2chain 'A' and (resid 56 through 76 )
3X-RAY DIFFRACTION3chain 'A' and (resid 77 through 96 )
4X-RAY DIFFRACTION4chain 'A' and (resid 97 through 119 )
5X-RAY DIFFRACTION5chain 'A' and (resid 120 through 155 )
6X-RAY DIFFRACTION6chain 'A' and (resid 156 through 221 )
7X-RAY DIFFRACTION7chain 'A' and (resid 222 through 264 )
8X-RAY DIFFRACTION8chain 'A' and (resid 265 through 276 )
9X-RAY DIFFRACTION9chain 'B' and (resid 41 through 55 )
10X-RAY DIFFRACTION10chain 'B' and (resid 56 through 78 )
11X-RAY DIFFRACTION11chain 'B' and (resid 79 through 139 )
12X-RAY DIFFRACTION12chain 'B' and (resid 140 through 221 )
13X-RAY DIFFRACTION13chain 'B' and (resid 222 through 276 )

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