[English] 日本語
Yorodumi- PDB-6alm: VioC L-arginine hydroxylase bound to Fe(II), L-arginine, and 2-OX... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6alm | ||||||
---|---|---|---|---|---|---|---|
Title | VioC L-arginine hydroxylase bound to Fe(II), L-arginine, and 2-OXO-GLUTARIC ACID | ||||||
Components | Alpha-ketoglutarate-dependent L-arginine hydroxylase | ||||||
Keywords | OXIDOREDUCTASE / hydroxylase / 2-oxo-glutarate / iron | ||||||
Function / homology | Function and homology information L-arginine hydroxylase / 2-oxoglutarate, L-arginine oxygenase (succinate-forming) activity / 2-oxoglutarate-dependent dioxygenase activity / antibiotic biosynthetic process / iron ion binding / membrane Similarity search - Function | ||||||
Biological species | Streptomyces vinaceus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Dunham, N.P. / Mitchell, A.J. / Boal, A.K. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: J. Am. Chem. Soc. / Year: 2017 Title: Visualizing the Reaction Cycle in an Iron(II)- and 2-(Oxo)-glutarate-Dependent Hydroxylase. Authors: Mitchell, A.J. / Dunham, N.P. / Martinie, R.J. / Bergman, J.A. / Pollock, C.J. / Hu, K. / Allen, B.D. / Chang, W.C. / Silakov, A. / Bollinger, J.M. / Krebs, C. / Boal, A.K. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6alm.cif.gz | 91.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6alm.ent.gz | 64.6 KB | Display | PDB format |
PDBx/mmJSON format | 6alm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/al/6alm ftp://data.pdbj.org/pub/pdb/validation_reports/al/6alm | HTTPS FTP |
---|
-Related structure data
Related structure data | 6alnC 6aloC 6alpC 6alqC 6alrC 2wboS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 43310.418 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces vinaceus (bacteria) / Gene: vioC / Production host: Escherichia coli (E. coli) / References: UniProt: Q6WZB0, L-arginine hydroxylase |
---|---|
#2: Chemical | ChemComp-FE2 / |
#3: Chemical | ChemComp-AKG / |
#4: Chemical | ChemComp-ARG / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.84 Å3/Da / Density % sol: 33.25 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 1 M 2-oxoglutarate, 0.1 M Tris pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 19, 2014 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.6→50 Å / Num. obs: 40551 / % possible obs: 97.4 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.02 / Rrim(I) all: 0.057 / Χ2: 0.714 / Net I/σ(I): 8.1 / Num. measured all: 311707 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2WBO Resolution: 1.6→50 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.247 / SU ML: 0.078 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.109 / ESU R Free: 0.106 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 69.17 Å2 / Biso mean: 20.377 Å2 / Biso min: 11.95 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.6→50 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.598→1.64 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|