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Yorodumi- PDB-4rhf: Crystal structure of UbiX mutant V47S from Colwellia psychrerythr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4rhf | ||||||
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Title | Crystal structure of UbiX mutant V47S from Colwellia psychrerythraea 34H | ||||||
Components | 3-octaprenyl-4-hydroxybenzoate carboxy-lyase | ||||||
Keywords | LYASE / Rossmann fold / decarboxylation | ||||||
Function / homology | Function and homology information flavin prenyltransferase / flavin prenyltransferase activity / lyase activity / nucleotide binding Similarity search - Function | ||||||
Biological species | Colwellia psychrerythraea 34H (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.764 Å | ||||||
Authors | Do, H. / Kim, S.J. / Lee, C.W. / Kim, H.-W. / Park, H.H. / Kim, H.M. / Park, H. / Park, H.J. / Lee, J.H. | ||||||
Citation | Journal: Sci Rep / Year: 2015 Title: Crystal structure of UbiX, an aromatic acid decarboxylase from the psychrophilic bacterium Colwellia psychrerythraea that undergoes FMN-induced conformational changes. Authors: Do, H. / Kim, S.J. / Lee, C.W. / Kim, H.W. / Park, H.H. / Kim, H.M. / Park, H. / Park, H. / Lee, J.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4rhf.cif.gz | 52.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4rhf.ent.gz | 37.7 KB | Display | PDB format |
PDBx/mmJSON format | 4rhf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rh/4rhf ftp://data.pdbj.org/pub/pdb/validation_reports/rh/4rhf | 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: 22842.277 Da / Num. of mol.: 1 / Mutation: V47S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Colwellia psychrerythraea 34H (bacteria) Gene: ubiX, CPS_0408 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q489U8, Lyases; Carbon-carbon lyases; Carboxy-lyases | ||
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#2: Chemical | #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: 3.39 Å3/Da / Density % sol: 63.77 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.4 Details: 0.1 M tri-sodium citrate, pH 5.4, 0.5 M ammonium sulfate, 1.2 M lithium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97952 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 7, 2013 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97952 Å / Relative weight: 1 |
Reflection | Resolution: 1.764→97.6 Å / Num. all: 30802 / Num. obs: 30737 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 40.5 % / Rmerge(I) obs: 0.136 / Net I/σ(I): 26.8 |
Reflection shell | Resolution: 1.764→1.86 Å / Redundancy: 39.9 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 13.7 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.764→97.6 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.892 / SU B: 2.216 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.112 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: 24.39 Å2
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Refinement step | Cycle: LAST / Resolution: 1.764→97.6 Å
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Refine LS restraints |
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