+Open data
-Basic information
Entry | Database: PDB / ID: 8hp5 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of (S)-2-haloacid dehalogenase | ||||||
Components | (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: 2.5 Å | ||||||
Authors | Yang, Q. / Wang, L. / Xu, X. / Xing, X. / Zhou, J. | ||||||
Funding support | China, 1items
| ||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8hp5.cif.gz | 168.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8hp5.ent.gz | 130.7 KB | Display | PDB format |
PDBx/mmJSON format | 8hp5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hp/8hp5 ftp://data.pdbj.org/pub/pdb/validation_reports/hp/8hp5 | HTTPS FTP |
---|
-Related structure data
Related structure data | 8hp6C 8hp7C C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | 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 | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.95 Å3/Da / Density % sol: 58.24 % |
---|---|
Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M SPG pH 7.0, 20% PEG1500 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 24, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→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 shell | Resolution: 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 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method 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
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→42.09 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|