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Yorodumi- PDB-1k63: Complex of hydrolytic haloalkane dehalogenase linb from sphingomo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1k63 | ||||||
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Title | Complex of hydrolytic haloalkane dehalogenase linb from sphingomonas paucimobilis with UT26 2-BROMO-2-PROPENE-1-OL 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 | 1k63.cif.gz | 84.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1k63.ent.gz | 61.5 KB | Display | PDB format |
PDBx/mmJSON format | 1k63.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1k63_validation.pdf.gz | 433.3 KB | Display | wwPDB validaton report |
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Full document | 1k63_full_validation.pdf.gz | 435.2 KB | Display | |
Data in XML | 1k63_validation.xml.gz | 17.9 KB | Display | |
Data in CIF | 1k63_validation.cif.gz | 28.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k6/1k63 ftp://data.pdbj.org/pub/pdb/validation_reports/k6/1k63 | HTTPS FTP |
-Related structure data
Related structure data | 1iz7C 1iz8C 1k5pSC 1k6eC 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
-Protein , 1 types, 1 molecules A
#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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-Non-polymers , 5 types, 471 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | BR(1001) AND CL(1003) ARE IN ALTERNATE CONFORMATIONS OF EACH OTHER. CL(1004) AND BR(1002) ARE IN ...BR(1001) AND CL(1003) ARE IN ALTERNATE CONFORMATI |
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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: 1.63 Å3/Da / Density % sol: 24.15 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.2 Details: PEG 4000, magnesium chloride, TRIS , pH 8.20, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54179 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 2001 / Details: MONOCHROMATOR AND MIRRORS |
Radiation | Monochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54179 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→27.8 Å / Num. all: 23055 / Num. obs: 23055 / % possible obs: 93.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 7.2 Å2 / Rmerge(I) obs: 0.117 / Net I/σ(I): 11.859 |
Reflection shell | Resolution: 1.8→1.98 Å / Redundancy: 4 % / Rmerge(I) obs: 0.281 / Mean I/σ(I) obs: 4.7 / Num. unique all: 4506 / % possible all: 83.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1K5P Resolution: 1.8→27.8 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 365901.69 / 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: 77.76 Å2 / ksol: 0.374018 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 12 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→27.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.98 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 4
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Xplor file |
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