[English] 日本語
Yorodumi- PDB-6sf5: Mn-containing form of the ribonucleotide reductase NrdB protein f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6sf5 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Mn-containing form of the ribonucleotide reductase NrdB protein from Leeuwenhoekiella blandensis | ||||||||||||
Components | Ribonucleoside-diphosphate reductase, beta subunit 1 | ||||||||||||
Keywords | METAL BINDING PROTEIN / ribonucleotide reductase apoprotein manganese binding redox protein deoxyribonucleotide synthesis | ||||||||||||
Function / homology | Function and homology information ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / ATP binding / metal ion binding Similarity search - Function | ||||||||||||
Biological species | Leeuwenhoekiella blandensis (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||||||||
Authors | Hasan, M. / Rozman Grinberg, I. / Sjoberg, B.M. / Logan, D.T. | ||||||||||||
Funding support | Sweden, 3items
| ||||||||||||
Citation | Journal: J.Biol.Inorg.Chem. / Year: 2019 Title: Class Id ribonucleotide reductase utilizes a Mn2(IV,III) cofactor and undergoes large conformational changes on metal loading. Authors: Rozman Grinberg, I. / Berglund, S. / Hasan, M. / Lundin, D. / Ho, F.M. / Magnuson, A. / Logan, D.T. / Sjoberg, B.M. / Berggren, G. | ||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6sf5.cif.gz | 266.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6sf5.ent.gz | 215.4 KB | Display | PDB format |
PDBx/mmJSON format | 6sf5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6sf5_validation.pdf.gz | 2.3 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6sf5_full_validation.pdf.gz | 2.3 MB | Display | |
Data in XML | 6sf5_validation.xml.gz | 25.2 KB | Display | |
Data in CIF | 6sf5_validation.cif.gz | 37.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sf/6sf5 ftp://data.pdbj.org/pub/pdb/validation_reports/sf/6sf5 | HTTPS FTP |
-Related structure data
Related structure data | 6sf4SC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 40577.906 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leeuwenhoekiella blandensis (bacteria) / Gene: MED217_17135 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): /pET28a(+) References: UniProt: A3XHF9, ribonucleoside-diphosphate reductase #2: Chemical | ChemComp-MN / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.13 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: Protein at 7.5 mg/ml in 50 mM Tris-HCl pH 7.8, 300 mM NaCl, 10% glycerol, 20 mM MgCl2, 2 mM tris(2-carboxyethyl)phosphine (TCEP) and 10 mM MnCl2. 200+200 nl sitting drops. Precipitant 0.1 M ...Details: Protein at 7.5 mg/ml in 50 mM Tris-HCl pH 7.8, 300 mM NaCl, 10% glycerol, 20 mM MgCl2, 2 mM tris(2-carboxyethyl)phosphine (TCEP) and 10 mM MnCl2. 200+200 nl sitting drops. Precipitant 0.1 M Bis-Tris pH 5.5, 25% w/v polyethylene glycol 3350. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 24, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→80.6 Å / Num. obs: 17348 / % possible obs: 99.9 % / Redundancy: 6.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.028 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 1.9→1.94 Å / Rmerge(I) obs: 1.137 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 3670 / CC1/2: 0.475 / Rpim(I) all: 0.658 / % possible all: 99.5 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6SF4 Resolution: 1.9→71.82 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.957 / SU R Cruickshank DPI: 0.126 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.13 / SU Rfree Blow DPI: 0.113 / SU Rfree Cruickshank DPI: 0.112
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.11 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.23 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→71.82 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.9→1.91 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|