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Yorodumi- PDB-1mj5: LINB (haloalkane dehalogenase) from sphingomonas paucimobilis UT2... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mj5 | ||||||
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Title | LINB (haloalkane dehalogenase) from sphingomonas paucimobilis UT26 at atomic resolution | ||||||
Components | 1,3,4,6-tetrachloro-1,4-cyclohexadiene hydrolase | ||||||
Keywords | HYDROLASE / LINB / Haloalkane dehalogenase / 1 / 3 / 4 / 6-tetrachloro-1 / 4-cyclohexadiene dehalogenase / gamma-Hexachlorocyclohexane degradation / alpha/beta-hydrolase / ultra high resolution | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.95 Å | ||||||
Authors | Oakley, A.J. / Damborsky, J. / Wilce, M.C. | ||||||
Citation | Journal: Biochemistry / Year: 2004 Title: Crystal structure of haloalkane dehalogenase LinB from Sphingomonas paucimobilis UT26 at 0.95 A resolution: dynamics of catalytic residues. Authors: Oakley, A.J. / Klvana, M. / Otyepka, M. / Nagata, Y. / Wilce, M.C. / Damborsky, J. #1: Journal: Biochemistry / Year: 2002 Title: Sphingomonas paucimobilis UT26: evidence for product- and water-mediated inhibition Authors: Oakley, A.J. / Prokop, Z. / Bohac, M. / Kmunicek, J. / Jedlicka, T. / Monincova, M. / Kuta-Smatanova, I. / Nagata, Y. / Damborsky, J. / Wilce, M.C.J. #2: Journal: Biochemistry / Year: 2000 Title: Crystal structure of the haloalkane dehalogenase from Sphingomonas paucimobilis UT26 Authors: Marek, J. / Vevodova, J. / Smatanova, I.K. / Nagata, Y. / Svensson, L.A. / Newman, J. / Takagi, M. / Damborsky, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mj5.cif.gz | 221.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mj5.ent.gz | 179.6 KB | Display | PDB format |
PDBx/mmJSON format | 1mj5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mj/1mj5 ftp://data.pdbj.org/pub/pdb/validation_reports/mj/1mj5 | HTTPS FTP |
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-Related structure data
Related structure data | 1cv2S S: Starting model for refinement |
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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: 33973.480 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sphingomonas paucimobilis (bacteria) / Strain: UT26 / Gene: LINB / Plasmid: pAQN / Production host: Escherichia coli (E. coli) / Strain (production host): HB101 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: 1.88 Å3/Da / Density % sol: 34.68 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 200 mM MgCl2, 100 mM Tris HCl pH 8.5, 20% (w/v) PEG 4,000, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 21, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 0.95→22.763 Å / Num. all: 305643 / Num. obs: 134890 / % possible obs: 83.4 % / Observed criterion σ(I): -2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 0.95→0.97 Å / Rmerge(I) obs: 0.367 / Mean I/σ(I) obs: 2.1 / % possible all: 79.7 |
Reflection | *PLUS Highest resolution: 0.95 Å / Lowest resolution: 50 Å / Num. obs: 134922 / Num. measured all: 305643 |
Reflection shell | *PLUS % possible obs: 79.7 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1CV2 Resolution: 0.95→22.763 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 0.95→22.763 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Highest resolution: 0.95 Å / Lowest resolution: 50 Å | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 0.95 Å / Lowest resolution: 0.97 Å / Rfactor Rfree: 0.1202 / Rfactor Rwork: 0.0912 |