+Open data
-Basic information
Entry | Database: PDB / ID: 4hr5 | ||||||
---|---|---|---|---|---|---|---|
Title | R2-like ligand-binding oxidase without metal cofactor | ||||||
Components | Ribonuleotide reductase small subunit | ||||||
Keywords | OXIDOREDUCTASE / R2-like ligand-binding oxidase / heterodinuclear Mn/Fe cofactor / ribonucleotide reductase R2 subunit fold / metalloprotein / manganese / iron / fatty acid/long-chain hydrocarbon ligand | ||||||
Function / homology | Function and homology information deoxyribonucleotide biosynthetic process / oxidoreductase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Geobacillus kaustophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.291 Å | ||||||
Authors | Griese, J.J. / Hogbom, M. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2013 Title: Direct observation of structurally encoded metal discrimination and ether bond formation in a heterodinuclear metalloprotein Authors: Griese, J.J. / Roos, K. / Cox, N. / Shafaat, H.S. / Branca, R.M.M. / Lehtio, J. / Graslund, A. / Lubitz, W. / Siegbahn, P.E.M. / Hogbom, M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4hr5.cif.gz | 116.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4hr5.ent.gz | 92.5 KB | Display | PDB format |
PDBx/mmJSON format | 4hr5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4hr5_validation.pdf.gz | 603.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4hr5_full_validation.pdf.gz | 606.6 KB | Display | |
Data in XML | 4hr5_validation.xml.gz | 12.3 KB | Display | |
Data in CIF | 4hr5_validation.cif.gz | 16 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hr/4hr5 ftp://data.pdbj.org/pub/pdb/validation_reports/hr/4hr5 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 36962.809 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus kaustophilus (bacteria) / Strain: HTA246 / Gene: GK2771 / Plasmid: pET-46 Ek/LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q5KW80, ribonucleoside-diphosphate reductase |
---|---|
#2: Chemical | ChemComp-PLM / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.26 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 17.5%(w/v) PEG 1500, 0.1M HEPES-Na, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.96 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Jan 25, 2012 |
Radiation | Monochromator: KMC-1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96 Å / Relative weight: 1 |
Reflection | Resolution: 2.29→30 Å / Num. all: 16220 / Num. obs: 16220 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 14.6 % / Biso Wilson estimate: 54.307 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 25.87 |
Reflection shell | Resolution: 2.29→2.43 Å / Redundancy: 14.7 % / Rmerge(I) obs: 0.754 / Mean I/σ(I) obs: 4.13 / Num. unique all: 2540 / % possible all: 99.1 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2.291→28.378 Å / SU ML: 0.22 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 26.12 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 71.4 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.291→28.378 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6
|