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Yorodumi- PDB-1zrn: INTERMEDIATE STRUCTURE OF L-2-HALOACID DEHALOGENASE WITH MONOCHLO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1zrn | ||||||
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Title | INTERMEDIATE STRUCTURE OF L-2-HALOACID DEHALOGENASE WITH MONOCHLOROACETATE | ||||||
Components | L-2-HALOACID DEHALOGENASE | ||||||
Keywords | DEHALOGENASE / HYDROLASE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pseudomonas sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.83 Å | ||||||
Authors | Li, Y.-F. / Hata, Y. / Fujii, T. / Hisano, T. / Nishihara, M. / Kurihara, T. / Esaki, N. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 1998 Title: Crystal structures of reaction intermediates of L-2-haloacid dehalogenase and implications for the reaction mechanism. Authors: Li, Y.F. / Hata, Y. / Fujii, T. / Hisano, T. / Nishihara, M. / Kurihara, T. / Esaki, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1zrn.cif.gz | 53.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zrn.ent.gz | 40.9 KB | Display | PDB format |
PDBx/mmJSON format | 1zrn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zr/1zrn ftp://data.pdbj.org/pub/pdb/validation_reports/zr/1zrn | HTTPS FTP |
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-Related structure data
Related structure data | 1zrmC 1judS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 26191.588 Da / Num. of mol.: 1 / Mutation: S175A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas sp. (bacteria) / Strain: YL / Gene: L-DEX_YL / Plasmid: PBA501 / Gene (production host): L-DEX_YL / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q53464, (S)-2-haloacid dehalogenase |
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#2: Chemical | ChemComp-ACY / |
#3: 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: 2.36 Å3/Da / Density % sol: 48 % | |||||||||||||||||||||||||
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Crystal grow | pH: 5.5 / Details: pH 5.5 | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Nov 26, 1996 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.83→15 Å / Num. obs: 17918 / % possible obs: 95 % / Observed criterion σ(I): 1 / Redundancy: 3.05 % / Biso Wilson estimate: 20.96 Å2 / Rmerge(I) obs: 0.0578 / Net I/σ(I): 11.47 |
Reflection shell | Resolution: 1.83→1.89 Å / Redundancy: 1.56 % / Rmerge(I) obs: 0.237 / % possible all: 90.2 |
Reflection | *PLUS Num. measured all: 54764 |
Reflection shell | *PLUS % possible obs: 90.2 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1JUD Resolution: 1.83→8 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 29.98 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.83→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.83→1.88 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.307 |