+Open data
-Basic information
Entry | Database: PDB / ID: 8hp6 | ||||||
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Title | Crystal structure of (S)-2-haloacid dehalogenase D12A mutant | ||||||
Components | (S)-2-haloacid dehalogenase(S)-2-haloacid dehalogenase | ||||||
Keywords | HYDROLASE / 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 / (S)-2-haloacid dehalogenase Function and homology information | ||||||
Biological species | Novosphingobium sp. MBES04 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Yang, Q. / Wang, L. / Xu, X. / Xing, X. / Zhou, J. | ||||||
Funding support | China, 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8hp6.cif.gz | 186.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8hp6.ent.gz | 135.4 KB | Display | PDB format |
PDBx/mmJSON format | 8hp6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hp/8hp6 ftp://data.pdbj.org/pub/pdb/validation_reports/hp/8hp6 | HTTPS FTP |
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-Related structure data
Related structure data | 8hp5C 8hp7C C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | 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 | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.51 Å3/Da / Density % sol: 64.93 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 3, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 |
-Processing
Software |
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Refinement | Method 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
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.58 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→36.8 Å
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Refine LS restraints |
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LS refinement shell |
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