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Yorodumi- PDB-1iz7: Re-refinement of the structure of hydrolytic haloalkane dehalogen... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1iz7 | ||||||
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Title | Re-refinement of the structure of hydrolytic haloalkane dehalogenase linb from sphingomonas paucimobilis UT26 AT 1.6 A resolution | ||||||
Components | HALOALKANE DEHALOGENASE, LINB | ||||||
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 / Resolution: 1.58 Å | ||||||
Authors | Streltsov, V.A. | ||||||
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. #1: Journal: Biochemistry / Year: 2000 Title: Crystal structure of the haloalkane dehalogenase from Sphingomonas paucimobilis UT26 Authors: Marek, J. / Vevodova, J. / Smatanova, I. / Nagata, Y. / Svensson, L.A. / Newman, J. / Takagi, M. / Damborsky, J. | ||||||
History |
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Remark 0 | This entry 1IZ7 reflects an alternative modeling of the structural data in r1cv2sf, In PDB entry ...This entry 1IZ7 reflects an alternative modeling of the structural data in r1cv2sf, In PDB entry 1IZ7 information in remark 200 series is based on the experiment described in pdb entry 1CV2 original data determined by author: J.MAREK,J.VEVODOVA,I.SMATANOVA,Y.NAGATA,L.A.SVENSSON,J.NEWMAN,M.TAKAGI,J.DAMBORSKY |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1iz7.cif.gz | 82.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1iz7.ent.gz | 60.3 KB | Display | PDB format |
PDBx/mmJSON format | 1iz7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1iz7_validation.pdf.gz | 427.7 KB | Display | wwPDB validaton report |
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Full document | 1iz7_full_validation.pdf.gz | 431.5 KB | Display | |
Data in XML | 1iz7_validation.xml.gz | 17.6 KB | Display | |
Data in CIF | 1iz7_validation.cif.gz | 27.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iz/1iz7 ftp://data.pdbj.org/pub/pdb/validation_reports/iz/1iz7 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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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) / Strain: UT26 / Plasmid: PMYLB1 / Production host: Escherichia coli (E. coli) / Strain (production host): HB101 References: UniProt: P51698, UniProt: D4Z2G1*PLUS, Hydrolases; Acting on halide bonds; In carbon-halide compounds | ||
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#2: Chemical | ChemComp-CL / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.2 % / Description: Author used the sf data from entry 1CV2. |
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Crystal grow | *PLUS Method: other / Details: re-refined 1CV2 |
-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | Biso Wilson estimate: 11.7 Å2 |
-Processing
Software | Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 1.58→19.86 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 4
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 58.6577 Å2 / ksol: 0.384471 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.58→19.86 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.58→1.74 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 4
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Xplor file |
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Refinement | *PLUS Rfactor Rwork: 0.14 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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