+Open data
-Basic information
Entry | Database: PDB / ID: 1bn7 | ||||||
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Title | HALOALKANE DEHALOGENASE FROM A RHODOCOCCUS SPECIES | ||||||
Components | HALOALKANE DEHALOGENASE | ||||||
Keywords | HYDROLASE / DEHALOGENASE / ALPHA/BETA-HYDROLASE / DHLA | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Rhodococcus sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.5 Å | ||||||
Authors | Newman, J. / Peat, T.S. / Richard, R. / Kan, L. / Swanson, P.E. / Affholter, J.A. / Holmes, I.H. / Schindler, J.F. / Unkefer, C.J. / Terwilliger, T.C. | ||||||
Citation | Journal: Biochemistry / Year: 1999 Title: Haloalkane dehalogenases: structure of a Rhodococcus enzyme. Authors: Newman, J. / Peat, T.S. / Richard, R. / Kan, L. / Swanson, P.E. / Affholter, J.A. / Holmes, I.H. / Schindler, J.F. / Unkefer, C.J. / Terwilliger, T.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bn7.cif.gz | 80.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bn7.ent.gz | 60.1 KB | Display | PDB format |
PDBx/mmJSON format | 1bn7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bn/1bn7 ftp://data.pdbj.org/pub/pdb/validation_reports/bn/1bn7 | HTTPS FTP |
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-Related 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: 33367.105 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodococcus sp. (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P59336, haloalkane dehalogenase |
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#2: Chemical | ChemComp-ACT / |
#3: 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: 2.43 Å3/Da / Density % sol: 38.8 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 5.5 / Details: pH 5.50 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 8 ℃ / pH: 7.5 / 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: NSLS / Beamline: X8C / Wavelength: 0.8157 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 1, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8157 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. obs: 52882 / % possible obs: 97.8 % / Observed criterion σ(I): 3 / Redundancy: 3.4 % / Biso Wilson estimate: 12.6 Å2 / Rsym value: 0.032 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 1.48→1.56 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 7.9 / Rsym value: 0.093 / % possible all: 87.5 |
Reflection | *PLUS Rmerge(I) obs: 0.032 |
Reflection shell | *PLUS % possible obs: 87.5 % / Rmerge(I) obs: 0.093 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 1.5→50 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3 / Stereochemistry target values: MLF
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Solvent computation | Bsol: 55.7 Å2 / ksol: 0.41 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.5→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.59 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: MLF / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 51664 / Rfactor obs: 0.159 / Rfactor Rfree: 0.179 / Rfactor Rwork: 0.159 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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