+Open data
-Basic information
Entry | Database: PDB / ID: 6a41 | ||||||
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Title | Dehalogenation enzyme | ||||||
Components | dehalogenase | ||||||
Keywords | OXIDOREDUCTASE / Dehalogenation | ||||||
Function / homology | Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily / Dehalogenase Function and homology information | ||||||
Biological species | Rhodospirillaceae (purple nonsulfur bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.97 Å | ||||||
Authors | Yin, B. / Yuan, A.Y. | ||||||
Citation | Journal: To Be Published Title: Structure of a new dehalogenase at 1.9 Angstroms resolution Authors: Yin, B. / Yuan, A.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6a41.cif.gz | 100.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6a41.ent.gz | 81.5 KB | Display | PDB format |
PDBx/mmJSON format | 6a41.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6a41_validation.pdf.gz | 420.1 KB | Display | wwPDB validaton report |
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Full document | 6a41_full_validation.pdf.gz | 421.2 KB | Display | |
Data in XML | 6a41_validation.xml.gz | 12.7 KB | Display | |
Data in CIF | 6a41_validation.cif.gz | 18.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a4/6a41 ftp://data.pdbj.org/pub/pdb/validation_reports/a4/6a41 | HTTPS FTP |
-Related structure data
Similar structure data |
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-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: 26209.137 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodospirillaceae (purple nonsulfur bacteria) Production host: Escherichia coli (E. coli) / References: UniProt: A0A5H1ZR29*PLUS |
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#2: 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: 2.61 Å3/Da / Density % sol: 52.87 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.2M Lithium Sulfate monohydrate, 0.1M Tris pH 8.5, 25% W/V Polyethylene Glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.9795 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Apr 1, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.97→70.96 Å / Num. obs: 18318 / % possible obs: 98.8 % / Redundancy: 6.3 % / Net I/σ(I): 50.6 |
Reflection shell | Resolution: 1.97→2.024 Å |
-Processing
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Refinement | Method to determine structure: SAD / Resolution: 1.97→70.96 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.94 / SU B: 4.895 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.122 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.122 Å2
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Refinement step | Cycle: 1 / Resolution: 1.97→70.96 Å
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Refine LS restraints |
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