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- PDB-8hp5: Crystal structure of (S)-2-haloacid dehalogenase -

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Basic information

Entry
Database: PDB / ID: 8hp5
TitleCrystal structure of (S)-2-haloacid dehalogenase
Components(S)-2-haloacid dehalogenase
KeywordsHYDROLASE / cyclic amino acid / ring-opening / detoxification
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 / 2-haloalkanoic acid dehalogenase
Function and homology information
Biological speciesNovosphingobium sp. MBES04 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsYang, Q. / Wang, L. / Xu, X. / Xing, X. / Zhou, J.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2018YFA0901900 China
CitationJournal: Catalysis Science And Technology / Year: 2023
Title: Enzymatic hydrolysis on L-azetidine-2-carboxylate ring opening
Authors: Xu, X. / Yang, Q. / Wang, L. / Zheng, J. / Gu, Y. / Xing, X.W. / Zhou, J.
History
DepositionDec 12, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 21, 2023Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)99,0666
Polymers98,8793
Non-polymers1863
Water7,782432
1
A: (S)-2-haloacid dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0222
Polymers32,9601
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: (S)-2-haloacid dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0222
Polymers32,9601
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: (S)-2-haloacid dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0222
Polymers32,9601
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)151.753, 151.753, 151.753
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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Components

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


Mass: 32959.812 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Novosphingobium sp. MBES04 (bacteria) / Gene: MBENS4_0996 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0S6WSA3
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 432 / 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: 2.95 Å3/Da / Density % sol: 58.24 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M SPG pH 7.0, 20% PEG1500

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.5→47.97 Å / Num. obs: 40320 / % possible obs: 99.7 % / Redundancy: 5.6 % / CC1/2: 0.969 / Rmerge(I) obs: 0.195 / Net I/σ(I): 5.5
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.545 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 4529 / CC1/2: 0.788 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2-4158refinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 2.5→42.09 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2156 2017 5.01 %
Rwork0.1657 --
obs0.1682 40258 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→42.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5853 0 12 432 6297
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076048
X-RAY DIFFRACTIONf_angle_d0.8838175
X-RAY DIFFRACTIONf_dihedral_angle_d14.0122247
X-RAY DIFFRACTIONf_chiral_restr0.049819
X-RAY DIFFRACTIONf_plane_restr0.0081086
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.560.30361630.21452723X-RAY DIFFRACTION100
2.56-2.630.28121510.19562675X-RAY DIFFRACTION100
2.63-2.710.2551320.19522714X-RAY DIFFRACTION99
2.71-2.80.24381690.19692651X-RAY DIFFRACTION99
2.8-2.90.2821300.18922744X-RAY DIFFRACTION100
2.9-3.010.23791210.18262735X-RAY DIFFRACTION100
3.01-3.150.26741450.18282734X-RAY DIFFRACTION100
3.15-3.320.22691380.18142708X-RAY DIFFRACTION100
3.32-3.520.19651490.15152743X-RAY DIFFRACTION100
3.53-3.80.20531490.15852713X-RAY DIFFRACTION99
3.8-4.180.17051180.1392738X-RAY DIFFRACTION99
4.18-4.780.17941500.1322756X-RAY DIFFRACTION100
4.78-6.010.1791530.15962764X-RAY DIFFRACTION100
6.02-42.090.20611490.16682843X-RAY DIFFRACTION98

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