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Yorodumi- PDB-5v0f: Crystal structure of C-As lyase with mutation K105A and substrate... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5v0f | ||||||
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Title | Crystal structure of C-As lyase with mutation K105A and substrate Roxarsone | ||||||
Components | Glyoxalase/bleomycin resistance protein/dioxygenase | ||||||
Keywords | OXIDOREDUCTASE / C-As lyase / Roxarsone | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thermomonospora curvata (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 Å | ||||||
Authors | Venkadesh, S. / Yoshinaga, M. / Sankaran, B. / Kandavelu, P. / Rosen, B.P. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Crystal structure of C-As lyase with mutation K105A and substrate Roxarsone. Authors: Venkadesh, S. / Yoshinaga, M. / Sankaran, B. / Kandavelu, P. / Rosen, B.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5v0f.cif.gz | 37.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5v0f.ent.gz | 23.8 KB | Display | PDB format |
PDBx/mmJSON format | 5v0f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5v0f_validation.pdf.gz | 446.3 KB | Display | wwPDB validaton report |
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Full document | 5v0f_full_validation.pdf.gz | 446.8 KB | Display | |
Data in XML | 5v0f_validation.xml.gz | 7.5 KB | Display | |
Data in CIF | 5v0f_validation.cif.gz | 9.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v0/5v0f ftp://data.pdbj.org/pub/pdb/validation_reports/v0/5v0f | HTTPS FTP |
-Related structure data
Related structure data | 5cb9S 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 13394.980 Da / Num. of mol.: 1 / Mutation: K105A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermomonospora curvata (strain ATCC 19995 / DSM 43183 / JCM 3096 / NBRC 15933 / NCIMB 10081 / Henssen B9) (bacteria) Strain: ATCC 19995 / DSM 43183 / JCM 3096 / NBRC 15933 / NCIMB 10081 / Henssen B9 Gene: Tcur_4156 / Production host: Escherichia coli (E. coli) / References: UniProt: D1A230 |
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#2: Chemical | ChemComp-RXO / |
#3: Chemical | ChemComp-FE / |
#4: Chemical | ChemComp-CL / |
#5: 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: 1.94 Å3/Da / Density % sol: 36.47 % |
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Crystal grow | Temperature: 294.2 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: 15% PEG 4000, 0.1 M Sodium acetate (pH 4.5) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9999 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 21, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9999 Å / Relative weight: 1 |
Reflection | Resolution: 2.23→41.77 Å / Num. obs: 5438 / % possible obs: 97.6 % / Redundancy: 6.7 % / Biso Wilson estimate: 31.2 Å2 / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.054 / Rrim(I) all: 0.145 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 2.23→2.35 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.863 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 782 / Rpim(I) all: 0.349 / Rrim(I) all: 0.96 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5CB9 Resolution: 2.23→39.384 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 25.58 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.23→39.384 Å
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Refine LS restraints |
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LS refinement shell |
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