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- PDB-6sf4: Apo form of the ribonucleotide reductase NrdB protein from Leeuwe... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6sf4 | ||||||||||||
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Title | Apo form of the ribonucleotide reductase NrdB protein from Leeuwenhoekiella blandensis | ||||||||||||
![]() | Ribonucleoside-diphosphate reductase, beta subunit 1 | ||||||||||||
![]() | METAL BINDING PROTEIN / ribonucleotide reductase apoprotein manganese binding redox protein deoxyribonucleotide synthesis | ||||||||||||
Function / homology | ![]() ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / ATP binding / metal ion binding Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Hasan, M. / Rozman Grinberg, I. / Sjoberg, B.M. / Logan, D.T. | ||||||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 144.3 KB | Display | ![]() |
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PDB format | ![]() | 111.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 421.8 KB | Display | ![]() |
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Full document | ![]() | 423.7 KB | Display | |
Data in XML | ![]() | 26.1 KB | Display | |
Data in CIF | ![]() | 39.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6sf5C ![]() 1syyS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 40577.906 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: CECT 7118 / CCUG 51940 / MED217 / Gene: MED217_17135 / Production host: ![]() ![]() References: UniProt: A3XHF9, ribonucleoside-diphosphate reductase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.18 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: Protein at 7.5 mg/ml in buffer containing 50 mM Tris-HCl pH 7.8, 300 mM NaCl, 10% glycerol, 20 mM MgCl2 and 2 mM tris(2-carboxyethyl)phosphine (TCEP). Precipitant 2.4 M sodium malonate ...Details: Protein at 7.5 mg/ml in buffer containing 50 mM Tris-HCl pH 7.8, 300 mM NaCl, 10% glycerol, 20 mM MgCl2 and 2 mM tris(2-carboxyethyl)phosphine (TCEP). Precipitant 2.4 M sodium malonate dibasic monohydrate pH 7.0. Drops 200+200 nl. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 14, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.85 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→49.94 Å / Num. obs: 74093 / % possible obs: 97.5 % / Redundancy: 17.5 % / Biso Wilson estimate: 32.5 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.035 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 14.8 % / Rmerge(I) obs: 2.299 / Mean I/σ(I) obs: 1 / Num. unique obs: 3025 / CC1/2: 0.538 / Rpim(I) all: 0.854 / % possible all: 76.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1SYY Resolution: 1.7→49.9 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.954 / SU R Cruickshank DPI: 0.096 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.1 / SU Rfree Blow DPI: 0.091 / SU Rfree Cruickshank DPI: 0.089
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Displacement parameters | Biso mean: 35.15 Å2
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Refine analyze | Luzzati coordinate error obs: 0.22 Å | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→49.9 Å
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