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- PDB-8hp6: Crystal structure of (S)-2-haloacid dehalogenase D12A mutant -

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Basic information

Entry
Database: PDB / ID: 8hp6
TitleCrystal structure of (S)-2-haloacid dehalogenase D12A mutant
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: 2.2 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)98,8166
Polymers98,7473
Non-polymers693
Water11,926662
1
A: (S)-2-haloacid dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9392
Polymers32,9161
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: (S)-2-haloacid dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9392
Polymers32,9161
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: (S)-2-haloacid dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9392
Polymers32,9161
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)151.726, 151.726, 151.726
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
Space group name HallP2ac2ab3
Symmetry operation#1: x,y,z
#2: z,x,y
#3: y,z,x
#4: -y+1/2,-z,x+1/2
#5: z+1/2,-x+1/2,-y
#6: -y,z+1/2,-x+1/2
#7: -z+1/2,-x,y+1/2
#8: -z,x+1/2,-y+1/2
#9: y+1/2,-z+1/2,-x
#10: x+1/2,-y+1/2,-z
#11: -x,y+1/2,-z+1/2
#12: -x+1/2,-y,z+1/2
Components on special symmetry positions
IDModelComponents
11A-664-

HOH

21A-667-

HOH

31B-584-

HOH

41B-586-

HOH

51B-588-

HOH

61C-607-

HOH

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Components

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


Mass: 32915.801 Da / Num. of mol.: 3 / Mutation: D12A
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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 662 / 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: 3.51 Å3/Da / Density % sol: 64.93 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop
Details: 1.2 M Potassium sodium tartrate tetrahydrate, 0.1 M Bis-Tris propane pH 7.0

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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: Sep 3, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.2→47.98 Å / Num. obs: 59134 / % possible obs: 100 % / Redundancy: 19.1 % / Biso Wilson estimate: 35.56 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.123 / Net I/σ(I): 20.8
Reflection shellResolution: 2.2→2.26 Å / Rmerge(I) obs: 0.984 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 4557 / CC1/2: 0.875 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 2.2→36.8 Å / SU ML: 0.2372 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.3806
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2012 2910 4.93 %
Rwork0.1661 56158 -
obs0.1678 59068 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.58 Å2
Refinement stepCycle: LAST / Resolution: 2.2→36.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5844 0 3 662 6509
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00786028
X-RAY DIFFRACTIONf_angle_d0.93578155
X-RAY DIFFRACTIONf_chiral_restr0.0519819
X-RAY DIFFRACTIONf_plane_restr0.00861083
X-RAY DIFFRACTIONf_dihedral_angle_d13.6382236
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.240.3061240.23912665X-RAY DIFFRACTION99.93
2.24-2.270.28161280.22682642X-RAY DIFFRACTION99.96
2.27-2.320.26851270.23062644X-RAY DIFFRACTION100
2.32-2.360.25261570.21832644X-RAY DIFFRACTION100
2.36-2.410.25121400.20262680X-RAY DIFFRACTION100
2.41-2.460.24471250.20582647X-RAY DIFFRACTION100
2.46-2.520.25621440.20032612X-RAY DIFFRACTION100
2.52-2.580.25171430.21582679X-RAY DIFFRACTION100
2.58-2.650.32741380.20532664X-RAY DIFFRACTION99.96
2.65-2.730.21781570.20982626X-RAY DIFFRACTION99.96
2.73-2.820.26241350.20212677X-RAY DIFFRACTION100
2.82-2.920.23271560.19742650X-RAY DIFFRACTION99.96
2.92-3.030.21661250.18842695X-RAY DIFFRACTION99.96
3.04-3.170.24031530.18952629X-RAY DIFFRACTION100
3.17-3.340.18651270.17122697X-RAY DIFFRACTION100
3.34-3.550.16981400.1522669X-RAY DIFFRACTION99.96
3.55-3.820.17681380.14272686X-RAY DIFFRACTION100
3.82-4.210.161400.12852714X-RAY DIFFRACTION100
4.21-4.810.15031310.11832690X-RAY DIFFRACTION99.93
4.81-6.060.15581280.13622750X-RAY DIFFRACTION99.97
6.06-36.80.16691540.14662798X-RAY DIFFRACTION99.43

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