+Open data
-Basic information
Entry | Database: PDB / ID: 4brz | ||||||
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Title | Haloalkane dehalogenase | ||||||
Components | HALOALKANE DEHALOGENASE | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | RHODOBACTERACEAE (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å | ||||||
Authors | Novak, H.R. / Sayer, C. / Isupov, M. / Gotz, D. / Spragg, A.M. / Littlechild, J.A. | ||||||
Citation | Journal: FEBS Lett. / Year: 2014 Title: Biochemical and Structural Characterisation of a Haloalkane Dehalogenase from a Marine Rhodobacteraceae. Authors: Novak, H.R. / Sayer, C. / Isupov, M.N. / Gotz, D. / Spragg, A.M. / Littlechild, J.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4brz.cif.gz | 139.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4brz.ent.gz | 109.5 KB | Display | PDB format |
PDBx/mmJSON format | 4brz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/br/4brz ftp://data.pdbj.org/pub/pdb/validation_reports/br/4brz | HTTPS FTP |
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-Related structure data
Related structure data | 4c6hC 1cv2S 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: 32557.631 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) RHODOBACTERACEAE (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA2 / References: UniProt: A0A067XG63*PLUS #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40 % / Description: NONE |
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Crystal grow | pH: 7 / Details: 0.3 M MGCL2, 0.1 M TRIS-HCL AND 30% PEG-4000, pH 7 |
-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9778 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 4, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9778 Å / Relative weight: 1 |
Reflection | Resolution: 1.67→44.4 Å / Num. obs: 61186 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 14.2 |
Reflection shell | Resolution: 1.67→1.71 Å / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2 / % possible all: 99.6 |
-Processing
Software | Name: REFMAC / Version: 5.7.0032 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1CV2 Resolution: 1.67→44.4 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.985 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.131 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD4 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.608 Å2
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Refinement step | Cycle: LAST / Resolution: 1.67→44.4 Å
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