+Open data
-Basic information
Entry | Database: PDB / ID: 1jud | ||||||
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Title | L-2-HALOACID DEHALOGENASE | ||||||
Components | L-2-HALOACID DEHALOGENASE | ||||||
Keywords | DEHALOGENASE / HYDROLASE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pseudomonas sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MIR / Resolution: 2.5 Å | ||||||
Authors | Hisano, T. / Hata, Y. / Fujii, T. / Liu, J.-Q. / Kurihara, T. / Esaki, N. / Soda, K. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 1996 Title: Crystal structure of L-2-haloacid dehalogenase from Pseudomonas sp. YL. An alpha/beta hydrolase structure that is different from the alpha/beta hydrolase fold. Authors: Hisano, T. / Hata, Y. / Fujii, T. / Liu, J.Q. / Kurihara, T. / Esaki, N. / Soda, K. #1: Journal: Proteins / Year: 1996 Title: Crystallization of L-2-Haloacid Dehalogenase from Pseudomonas Sp. Yl Authors: Hisano, T. / Hata, Y. / Fujii, T. / Kurihara, T. / Esaki, N. / Soda, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jud.cif.gz | 55.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jud.ent.gz | 40.4 KB | Display | PDB format |
PDBx/mmJSON format | 1jud.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1jud_validation.pdf.gz | 369.1 KB | Display | wwPDB validaton report |
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Full document | 1jud_full_validation.pdf.gz | 371 KB | Display | |
Data in XML | 1jud_validation.xml.gz | 5.9 KB | Display | |
Data in CIF | 1jud_validation.cif.gz | 8.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ju/1jud ftp://data.pdbj.org/pub/pdb/validation_reports/ju/1jud | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 26207.588 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas sp. (bacteria) / Strain: YL / Gene: L-DEX YL / Plasmid: PKK223-3 / Gene (production host): L-DEX YL / Production host: Escherichia coli (E. coli) / References: UniProt: Q53464, (S)-2-haloacid dehalogenase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48 % | |||||||||||||||||||||||||
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Crystal grow | pH: 5 / Details: pH 5.0 | |||||||||||||||||||||||||
Crystal | *PLUS | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 |
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Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Jan 7, 1995 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→43 Å / Num. obs: 8124 / % possible obs: 93 % / Observed criterion σ(I): 1 / Redundancy: 3.9 % / Rmerge(I) obs: 0.0397 |
Reflection shell | Resolution: 2.5→2.6 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.109 / % possible all: 90.3 |
Reflection | *PLUS Num. measured all: 31020 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.5→8 Å / σ(F): 2
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Displacement parameters | Biso mean: 14.14 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.25 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→8 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 14.143 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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