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Yorodumi- PDB-1k5p: Hydrolytic haloalkane dehalogenase LINB from sphingomonas paucimo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1k5p | ||||||
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Title | Hydrolytic haloalkane dehalogenase LINB from sphingomonas paucimobilis UT26 at 1.8A resolution | ||||||
Components | 1,3,4,6-tetrachloro-1,4-cyclohexadiene hydrolase | ||||||
Keywords | HYDROLASE / DEHALOGENASE / LINDANE / BIODEGRADATION / ALPHA/BETA-HYDROLASE | ||||||
Function / homology | Function and homology information haloalkane dehalogenase / haloalkane dehalogenase activity / response to toxic substance / periplasmic space Similarity search - Function | ||||||
Biological species | Sphingomonas paucimobilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Streltsov, V.A. / Damborsky, J. / Wilce, M.C.J. | ||||||
Citation | Journal: Biochemistry / Year: 2003 Title: Haloalkane dehalogenase LinB from Sphingomonas paucimobilis UT26: X-ray crystallographic studies of dehalogenation of brominated substrates Authors: Streltsov, V.A. / Prokop, Z. / Damborsky, J. / Nagata, Y. / Oakley, A. / Wilce, M.C.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1k5p.cif.gz | 83 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1k5p.ent.gz | 60 KB | Display | PDB format |
PDBx/mmJSON format | 1k5p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k5/1k5p ftp://data.pdbj.org/pub/pdb/validation_reports/k5/1k5p | HTTPS FTP |
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-Related structure data
Related structure data | 1iz7C 1iz8C 1k63C 1k6eC 1cv2S 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: 33013.410 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sphingomonas paucimobilis (bacteria) / Plasmid: PMYLB1 / Production host: Escherichia coli (E. coli) References: UniProt: P51698, UniProt: D4Z2G1*PLUS, haloalkane dehalogenase | ||||
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#2: Chemical | #3: Chemical | #4: 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: 1.73 Å3/Da / Density % sol: 28.23 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: PEG 4000, TRIS, magnesium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 14, 2000 / Details: mirrors |
Radiation | Monochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→34.77 Å / Num. all: 21294 / Num. obs: 21294 / % possible obs: 83.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12 % / Biso Wilson estimate: 14.1 Å2 / Rmerge(I) obs: 0.077 / Rsym value: 0.077 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 1.8→1.98 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 2.2 / Num. unique all: 3393 / Rsym value: 0.28 / % possible all: 60.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1CV2 Resolution: 1.8→34.77 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 325933.63 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Details: The structure was refined also with XTALVIEW.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 102.629 Å2 / ksol: 0.409013 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→34.77 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.98 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 4
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Xplor file |
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