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- PDB-8hp7: Crystal structure of (S)-2-haloacid dehalogenase K152A mutant tra... -

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Basic information

Entry
Database: PDB / ID: 8hp7
TitleCrystal structure of (S)-2-haloacid dehalogenase K152A mutant trapped with (2R)-4-amino-2-hydroxybutanoic acid
Components(S)-2-haloacid dehalogenase(S)-2-haloacid dehalogenase
KeywordsHYDROLASE / cyclic amino acid / ring-opening / detoxification
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 / GAMMA-AMINO-BUTANOIC ACID / (S)-2-haloacid dehalogenase
Function and homology information
Biological speciesNovosphingobium sp. MBES04 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 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 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond / Item: _atom_site.auth_atom_id / _atom_site.label_atom_id

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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)99,1398
Polymers98,7053
Non-polymers4335
Water15,547863
1
A: (S)-2-haloacid dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0052
Polymers32,9021
Non-polymers1031
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: (S)-2-haloacid dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0052
Polymers32,9021
Non-polymers1031
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: (S)-2-haloacid dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1294
Polymers32,9021
Non-polymers2273
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)145.987, 84.221, 102.356
Angle α, β, γ (deg.)90.00, 133.93, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-644-

HOH

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Components

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


Mass: 32901.711 Da / Num. of mol.: 3 / Mutation: K152A
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-ABU / GAMMA-AMINO-BUTANOIC ACID / GAMMA(AMINO)-BUTYRIC ACID / Γ-Aminobutyric acid


Mass: 103.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H9NO2 / Feature type: SUBJECT OF INVESTIGATION / Comment: neurotransmitter, inhibitor*YM
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 863 / Source method: isolated from a natural source / Formula: H2O
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: 2.72 Å3/Da / Density % sol: 54.77 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / Details: 200 mM Potassium nitrate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.43→41.02 Å / Num. obs: 153210 / % possible obs: 93.4 % / Redundancy: 7 % / CC1/2: 0.989 / Rmerge(I) obs: 0.173 / Net I/σ(I): 8.4
Reflection shellResolution: 1.43→1.45 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.564 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 7519 / CC1/2: 0.919 / % possible all: 93.1

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Processing

Software
NameVersionClassification
PHENIX1.20.1-4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 1.43→36.48 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2106 7231 4.73 %
Rwork0.1927 --
obs0.1936 152719 92.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.43→36.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5874 0 8 863 6745
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076167
X-RAY DIFFRACTIONf_angle_d0.8968357
X-RAY DIFFRACTIONf_dihedral_angle_d13.5712313
X-RAY DIFFRACTIONf_chiral_restr0.078838
X-RAY DIFFRACTIONf_plane_restr0.0091116
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.43-1.450.25592730.23334763X-RAY DIFFRACTION93
1.45-1.460.23612380.23534866X-RAY DIFFRACTION93
1.46-1.480.2852100.23454866X-RAY DIFFRACTION93
1.48-1.50.21512230.19994801X-RAY DIFFRACTION93
1.5-1.520.2252050.19774894X-RAY DIFFRACTION93
1.52-1.540.22242530.19554772X-RAY DIFFRACTION92
1.54-1.560.23142180.1884735X-RAY DIFFRACTION90
1.56-1.590.22362180.19264539X-RAY DIFFRACTION87
1.59-1.610.20592500.18294821X-RAY DIFFRACTION94
1.61-1.640.20762480.18044903X-RAY DIFFRACTION94
1.64-1.670.21512240.18864949X-RAY DIFFRACTION94
1.67-1.70.20862430.17864928X-RAY DIFFRACTION94
1.7-1.730.20092680.18684869X-RAY DIFFRACTION94
1.73-1.760.19962330.18244916X-RAY DIFFRACTION94
1.76-1.80.21252110.18354900X-RAY DIFFRACTION93
1.8-1.840.22731960.18754842X-RAY DIFFRACTION92
1.84-1.890.22992220.20244525X-RAY DIFFRACTION87
1.89-1.940.36912590.34644568X-RAY DIFFRACTION88
1.94-20.23242620.18734944X-RAY DIFFRACTION95
2-2.060.21091940.17995078X-RAY DIFFRACTION96
2.06-2.140.19012820.17544907X-RAY DIFFRACTION95
2.14-2.220.18312410.18034921X-RAY DIFFRACTION94
2.22-2.320.29862790.27384742X-RAY DIFFRACTION92
2.32-2.450.18932470.18224588X-RAY DIFFRACTION88
2.45-2.60.19593000.18595006X-RAY DIFFRACTION97
2.6-2.80.21272580.18055042X-RAY DIFFRACTION96
2.8-3.080.20742460.18254977X-RAY DIFFRACTION95
3.08-3.530.18662170.17664702X-RAY DIFFRACTION89
3.53-4.440.15642610.16365136X-RAY DIFFRACTION97
4.44-36.480.17792520.1794988X-RAY DIFFRACTION93

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