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Yorodumi- PDB-1on2: Bacillus subtilis Manganese Transport Regulator (MntR), D8M Mutan... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1on2 | ||||||
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Title | Bacillus subtilis Manganese Transport Regulator (MntR), D8M Mutant, Bound to Manganese | ||||||
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 / DNA binding / cytoplasm Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.61 Å | ||||||
Authors | Glasfeld, A. / Guedon, E. / Helmann, J.D. / Brennan, R.G. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2003 Title: Structure of the Manganese-Bound Manganese Transport Regulator of Bacillus subtilis Authors: Glasfeld, A. / Guedon, E. / Helmann, J.D. / Brennan, R.G. | ||||||
History |
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Remark 999 | Authors informed that the individuals who originally sequenced the gene have submitted a revised ...Authors informed that the individuals who originally sequenced the gene have submitted a revised sequence to GenBank which identifies Glu as the correct residue at position 81. The corrected sequence has not yet been published. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1on2.cif.gz | 70.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1on2.ent.gz | 53 KB | Display | PDB format |
PDBx/mmJSON format | 1on2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/on/1on2 ftp://data.pdbj.org/pub/pdb/validation_reports/on/1on2 | HTTPS FTP |
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-Related 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: 16803.240 Da / Num. of mol.: 2 / Mutation: D8M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Plasmid: pHB7506 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL / References: UniProt: P54512 #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.97 Å3/Da / Density % sol: 37.47 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 8.5 Details: 30% PEG 400, 0.15 M Lithium sulfate, pH 8.5, VAPOR DIFFUSION, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.61→45.6 Å / Num. obs: 30208 / % possible obs: 91.6 % / Observed criterion σ(I): 2.4 / Rmerge(I) obs: 0.043 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 1.61→1.67 Å / Rmerge(I) obs: 0.266 / Mean I/σ(I) obs: 2.4 / % possible all: 61.8 |
Reflection | *PLUS Num. measured all: 101987 |
Reflection shell | *PLUS % possible obs: 62.8 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.61→45.6 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2.4
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.61→45.6 Å
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Refine LS restraints |
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Xplor file |
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Refinement | *PLUS % reflection Rfree: 5 % / Rfactor Rwork: 0.22 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_bond_d / Dev ideal: 0.005 |