+Open data
-Basic information
Entry | Database: PDB / ID: 4cf3 | ||||||
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Title | Mutagenesis of a Rhodobacteraceae L-haloacid dehalogenase | ||||||
Components | L-HALOACID DEHALOGENASE | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | RHODOBACTERACEAE (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å | ||||||
Authors | Novak, H.R. / Sayer, C. / Isupov, M.N. / Littlechild, J.A. | ||||||
Citation | Journal: To be Published Title: Mutagenesis of a Rhodobacteraceae L-Haloacid Dehalogenase Authors: Novak, H.R. / Sayer, C. / Isupov, M.N. / 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 | 4cf3.cif.gz | 187.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cf3.ent.gz | 150.6 KB | Display | PDB format |
PDBx/mmJSON format | 4cf3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4cf3_validation.pdf.gz | 472.6 KB | Display | wwPDB validaton report |
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Full document | 4cf3_full_validation.pdf.gz | 485.2 KB | Display | |
Data in XML | 4cf3_validation.xml.gz | 38.2 KB | Display | |
Data in CIF | 4cf3_validation.cif.gz | 52 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cf/4cf3 ftp://data.pdbj.org/pub/pdb/validation_reports/cf/4cf3 | HTTPS FTP |
-Related structure data
Related structure data | 4ce6C 4cf4C 4cf5C 4cnqC 2ymlS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 25737.301 Da / Num. of mol.: 4 / Mutation: YES 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): CODONPLUS-RIPL References: UniProt: M9P6K0, UniProt: R4GRT2*PLUS, (S)-2-haloacid dehalogenase #2: Chemical | ChemComp-TRS / #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: 2.03 Å3/Da / Density % sol: 39.31 % / Description: NONE |
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Crystal grow | pH: 8 / Details: pH 8 |
-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 2.16→36.86 Å / Num. obs: 46129 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 6 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 2.16→2.16 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2.5 / % possible all: 2.2 |
-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 2YML Resolution: 2.16→36.86 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.925 / SU B: 7.179 / SU ML: 0.18 / Cross valid method: THROUGHOUT / ESU R: 0.283 / ESU R Free: 0.228 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES 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: 42.544 Å2
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Refinement step | Cycle: LAST / Resolution: 2.16→36.86 Å
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