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Yorodumi- PDB-2f5c: Bacillus subtilis Manganese transport regulator (MNTR) bound to m... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2f5c | ||||||
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Title | Bacillus subtilis Manganese transport regulator (MNTR) bound to manganese, hexagonal crystal form | ||||||
Components | Transcriptional regulator mntR | ||||||
Keywords | TRANSCRIPTION / HELIX-TURN-HELIX / DNA-BINDING PROTEIN / METALLOREGULATORY PROTEIN | ||||||
Function / homology | Function and homology information intracellular manganese ion homeostasis / manganese ion binding / protein dimerization activity / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA binding / cytoplasm Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Kliegman, J.I. / Griner, S.L. / Helmann, J.D. / Brennan, R.G. / Glasfeld, A. | ||||||
Citation | Journal: Biochemistry / Year: 2006 Title: Structural Basis for the Metal-Selective Activation of the Manganese Transport Regulator of Bacillus subtilis. Authors: Kliegman, J.I. / Griner, S.L. / Helmann, J.D. / Brennan, R.G. / Glasfeld, A. | ||||||
History |
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Remark 999 | SEQUENCE THE AUTHOR MAINTAINS THAT THE CORRECT RESIDUE AT THIS LOCATION SHOULD BE GLU. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2f5c.cif.gz | 43.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2f5c.ent.gz | 29.5 KB | Display | PDB format |
PDBx/mmJSON format | 2f5c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f5/2f5c ftp://data.pdbj.org/pub/pdb/validation_reports/f5/2f5c | HTTPS FTP |
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-Related structure data
Related structure data | 2ev0C 2ev5C 2ev6C 2f5dC 2f5eC 2f5fC 1on1S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 16787.133 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: mntR / Plasmid: PHB7506 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL / References: UniProt: P54512 | ||||
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#2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.4 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 25% PEG 400, 0.12 M LITHIUM SULFATE, PH 8.50, 23 BP DUPLEX DNA PRESENT, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.1271 |
Detector | Type: NOIR-1 / Detector: CCD / Date: Apr 9, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1271 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→40 Å / Num. obs: 5959 / % possible obs: 92.6 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 29.1 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 6.6 |
Reflection shell | Resolution: 2.4→2.49 Å / Rmerge(I) obs: 0.323 / Mean I/σ(I) obs: 19.8 / % possible all: 48.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ON1 Resolution: 2.4→19.93 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 1586606.53 / Data cutoff high rms absF: 1586606.53 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 21.6918 Å2 / ksol: 0.334406 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→19.93 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.046 / Total num. of bins used: 6
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Xplor file |
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