[English] 日本語
Yorodumi- PDB-4rb2: Crystal structure of Magnetospirillum gryphiswaldense MSR-1 SeMet... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4rb2 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Magnetospirillum gryphiswaldense MSR-1 SeMet-Fur-Mn2+-feoAB1 operator | ||||||
Components |
| ||||||
Keywords | METAL BINDING PROTEIN/DNA / ferric uptake regulator (FUR) / metal ion activation / operator recognition / cooperativity / broad substrate recognition / DNA shape readout / METAL BINDING PROTEIN-DNA complex | ||||||
Function / homology | Function and homology information negative regulation of siderophore biosynthetic process / transcription cis-regulatory region binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / zinc ion binding / cytosol Similarity search - Function | ||||||
Biological species | Magnetospirillum gryphiswaldense (magnetotactic) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.82 Å | ||||||
Authors | Deng, Z. / Chen, Z. | ||||||
Citation | Journal: Nat Commun Title: Mechanistic insights into metal ion activation and operator recognition by the ferric uptake regulator. Authors: Deng, Z. / Wang, Q. / Liu, Z. / Zhang, M. / Machado, A.C. / Chiu, T.P. / Feng, C. / Zhang, Q. / Yu, L. / Qi, L. / Zheng, J. / Wang, X. / Huo, X. / Qi, X. / Li, X. / Wu, W. / Rohs, R. / Li, Y. / Chen, Z. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4rb2.cif.gz | 95.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4rb2.ent.gz | 67.9 KB | Display | PDB format |
PDBx/mmJSON format | 4rb2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4rb2_validation.pdf.gz | 452.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4rb2_full_validation.pdf.gz | 458.5 KB | Display | |
Data in XML | 4rb2_validation.xml.gz | 13.5 KB | Display | |
Data in CIF | 4rb2_validation.cif.gz | 17.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rb/4rb2 ftp://data.pdbj.org/pub/pdb/validation_reports/rb/4rb2 | HTTPS FTP |
-Related structure data
Related structure data | 4raySC 4razC 4rb0C 4rb1C 4rb3C 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: DNA chain | Mass: 7646.970 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||||
---|---|---|---|---|---|
#2: DNA chain | Mass: 7705.022 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||||
#3: Protein | Mass: 16807.314 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Magnetospirillum gryphiswaldense (magnetotactic) Strain: MSR-1 v2 / Gene: Fur, MGMSRv2_3137 / Production host: Escherichia coli (E. coli) / References: UniProt: V6F4Q0 #4: Chemical | ChemComp-MN / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
---|
-Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.32 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 130 K | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: BSRF / Beamline: 1W2B / Wavelength: 0.9793, 0.9795, 1.000 | ||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 11, 2012 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
| ||||||||||||
Reflection | Resolution: 2.82→50 Å / Num. all: 12295 / Num. obs: 11230 / % possible obs: 91.4 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 | ||||||||||||
Reflection shell | Resolution: 2.82→2.87 Å / % possible all: 92.4 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MAD Starting model: PDB entry 4RAY Resolution: 2.82→45.73 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.897 / SU B: 17.896 / SU ML: 0.341 / Cross valid method: THROUGHOUT / σ(F): 3 / ESU R Free: 0.44 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 85.68 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.82→45.73 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|