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Yorodumi- PDB-1g42: STRUCTURE OF 1,3,4,6-TETRACHLORO-1,4-CYCLOHEXADIENE HYDROLASE (LI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1g42 | ||||||
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Title | STRUCTURE OF 1,3,4,6-TETRACHLORO-1,4-CYCLOHEXADIENE HYDROLASE (LINB) FROM SPHINGOMONAS PAUCIMOBILIS COMPLEXED WITH 1,2-DICHLOROPROPANE | ||||||
Components | 1,3,4,6-TETRACHLORO-1,4-CYCLOHEXADIENE HYDROLASE | ||||||
Keywords | HYDROLASE / LinB dehalogenase alpha/beta-hydrolase halocarbons | ||||||
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 | Oakley, A.J. / Prokop, Z. / Bohac, M. / Kmunicek, J. / Jedlicka, T. / Monincova, M. / Kuta-Smatanova, I. / Nagata, Y. / Damborsky, J. / Wilce, M.C.J. | ||||||
Citation | Journal: Biochemistry / Year: 2002 Title: Exploring the structure and activity of haloalkane dehalogenase from 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. #1: 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 | 1g42.cif.gz | 85.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1g42.ent.gz | 60.6 KB | Display | PDB format |
PDBx/mmJSON format | 1g42.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1g42_validation.pdf.gz | 458 KB | Display | wwPDB validaton report |
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Full document | 1g42_full_validation.pdf.gz | 460.1 KB | Display | |
Data in XML | 1g42_validation.xml.gz | 17.4 KB | Display | |
Data in CIF | 1g42_validation.cif.gz | 27 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g4/1g42 ftp://data.pdbj.org/pub/pdb/validation_reports/g4/1g42 | HTTPS FTP |
-Related structure data
Related structure data | 1g4hC 1g5fC 1cv2S C: citing same article (ref.) 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 on special symmetry positions |
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Details | The asymmetric unit contains the functional monomer |
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 33171.652 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sphingomonas paucimobilis (bacteria) / Gene: LINB / Plasmid: PMLBH6 / 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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-Non-polymers , 5 types, 415 molecules
#2: Chemical | ChemComp-ACT / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-CL / | #5: Chemical | #6: 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: 2.03 Å3/Da / Density % sol: 39.09 % | ||||||||||||||||||||
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, hanging drop / pH: 8.9 Details: 0.1 M Tris-HCl pH 8.9, 18-20%(w/v) PEG 6000, 0.2 M calcium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 278K | ||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 13, 2000 / Details: Ni Mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. all: 25682 / Num. obs: 55091 / % possible obs: 97 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 2.21 % / Biso Wilson estimate: 11.4 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 12.75 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 2.06 % / Rmerge(I) obs: 0.241 / Mean I/σ(I) obs: 2.97 / Num. unique all: 2402 / % possible all: 95.7 |
Reflection | *PLUS Num. obs: 24918 / Num. measured all: 55091 |
Reflection shell | *PLUS % possible obs: 95.7 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1CV2 Resolution: 1.8→18.78 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1468372.72 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 60.67 Å2 / ksol: 0.369 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→18.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 5.1 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 13.2 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.244 / Rfactor Rwork: 0.233 |