[English] 日本語
Yorodumi- PDB-6d9f: Protein 60 with aldehyde deformylating oxidase activity from Kita... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6d9f | ||||||
---|---|---|---|---|---|---|---|
Title | Protein 60 with aldehyde deformylating oxidase activity from Kitasatospora setae | ||||||
Components | Putative VlmB homolog | ||||||
Keywords | LYASE / Ferritin-like | ||||||
Function / homology | Ribonucleotide reductase-like / Ferritin-like superfamily / oxidoreductase activity / : / Putative VlmB homolog Function and homology information | ||||||
Biological species | Kitasatospora setae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.03 Å | ||||||
Authors | Arenas, R. / Wilson, D.K. / Mak, W.S. / Siegel, J.B. | ||||||
Citation | Journal: Biochemistry / Year: 2020 Title: Discovery, Design, and Structural Characterization of Alkane-Producing Enzymes across the Ferritin-like Superfamily. Authors: Mak, W.S. / Wang, X. / Arenas, R. / Cui, Y. / Bertolani, S. / Deng, W.Q. / Tagkopoulos, I. / Wilson, D.K. / Siegel, J.B. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6d9f.cif.gz | 138.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6d9f.ent.gz | 108.2 KB | Display | PDB format |
PDBx/mmJSON format | 6d9f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d9/6d9f ftp://data.pdbj.org/pub/pdb/validation_reports/d9/6d9f | HTTPS FTP |
---|
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 36919.941 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Kitasatospora setae (strain ATCC 33774 / DSM 43861 / JCM 3304 / KCC A-0304 / NBRC 14216 / KM-6054) (bacteria) Strain: ATCC 33774 / DSM 43861 / JCM 3304 / KCC A-0304 / NBRC 14216 / KM-6054 Gene: vlmB, KSE_09070 / Production host: Escherichia coli (E. coli) / References: UniProt: E4N6B3 #2: Chemical | ChemComp-FE / #3: Chemical | #4: Chemical | ChemComp-EDO / #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.32 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.075 M TRIS hydrochloride pH 8.5, 1.5 M Ammonium sulfate, 25% v/v Glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 21, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 2.03→66.76 Å / Num. obs: 50138 / % possible obs: 99.8 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 15.8 |
Reflection shell | Resolution: 2.03→2.08 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.362 / Mean I/σ(I) obs: 4.8 / Num. unique obs: 3667 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2.03→66.76 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.937 / SU B: 5.3 / SU ML: 0.137 / Cross valid method: THROUGHOUT / ESU R: 0.179 / ESU R Free: 0.159 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.396 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.03→66.76 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|