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Yorodumi- PDB-1d07: Hydrolytic haloalkane dehalogenase linb from sphingomonas paucimo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1d07 | ||||||
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Title | Hydrolytic haloalkane dehalogenase linb from sphingomonas paucimobilis UT26 with 1,3-propanediol, a product of debromidation of dibrompropane, at 2.0A resolution | ||||||
Components | HALOALKANE DEHALOGENASE | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Marek, J. / Vevodova, J. / Damborsky, J. / Smatanova, I. / Svensson, L.A. / Newman, J. / Nagata, Y. / Takagi, M. | ||||||
Citation | 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. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1999 Title: Crystallization and Preliminary X-Ray Diffraction Analysis of Haloalkane Dehalogenase Linb from Sphingomonas Paucimobilis Ut26 Authors: Smatanova, I. / Nagata, Y. / Svensson, L.A. / Takagi, M. / Marek, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1d07.cif.gz | 77.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1d07.ent.gz | 55.7 KB | Display | PDB format |
PDBx/mmJSON format | 1d07.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1d07_validation.pdf.gz | 415.2 KB | Display | wwPDB validaton report |
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Full document | 1d07_full_validation.pdf.gz | 422.7 KB | Display | |
Data in XML | 1d07_validation.xml.gz | 9.4 KB | Display | |
Data in CIF | 1d07_validation.cif.gz | 14.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d0/1d07 ftp://data.pdbj.org/pub/pdb/validation_reports/d0/1d07 | HTTPS FTP |
-Related structure data
Related structure data | 1cv2SC 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: 33144.609 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sphingomonas paucimobilis (bacteria) / Strain: UT26 / Plasmid: PMYLB1 / 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 | ChemComp-PDO / | #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: 2.07 Å3/Da / Density % sol: 40.2 % | ||||||||||||||||||||
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, hanging drop / pH: 8.9 Details: 19% (W/V) PEG 6000, 100 MM TRIS-HCL, 200MM CA ACETATE, PH=8.9 VAPOR DIFFUSION, HANGING DROP. CRYSTAL WAS SOAKED 4 HOURS IN RESERVOIR LIQUOR WITH 25MM 1,3-DIBROMPROPANE AT 278K | ||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / Details: used microseeding | ||||||||||||||||||||
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: MAX II / Beamline: I711 / Wavelength: 0.9 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 4, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. obs: 16801 / % possible obs: 86.6 % / Redundancy: 7.67 % / Biso Wilson estimate: 10.9 Å2 / Rmerge(I) obs: 0.113 / Net I/σ(I): 12.37 |
Reflection shell | Resolution: 2→2.13 Å / Redundancy: 7.64 % / Rmerge(I) obs: 0.296 / Mean I/σ(I) obs: 4.55 / % possible all: 99.8 |
Reflection | *PLUS Lowest resolution: 20 Å / Rmerge(I) obs: 0.113 |
Reflection shell | *PLUS Highest resolution: 2 Å / % possible obs: 99.8 % / Rmerge(I) obs: 0.289 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1CV2 Resolution: 2→20 Å / Rfactor Rfree error: 0.007 / Num. parameters: 1036 / Num. restraintsaints: 971 / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: MOEWS & KRETSINGER: J.MOL.BIOL. 91 (1973) 201-228 | |||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.8 Å2 | |||||||||||||||||||||||||||||||||
Refine analyze | Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2574
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.022
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Software | *PLUS Name: SHELXL / Version: 96 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 20 Å / Rfactor all: 0.18 / Rfactor obs: 0.169 / Rfactor Rfree: 0.258 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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