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Yorodumi- PDB-4m33: Crystal structure of gated-pore mutant H141D of second DNA-Bindin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4m33 | ||||||
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Title | Crystal structure of gated-pore mutant H141D of second DNA-Binding protein under starvation from Mycobacterium smegmatis | ||||||
Components | Putative starvation-induced DNA protecting protein/Ferritin and Dps | ||||||
Keywords | DNA BINDING PROTEIN / ferritin-like fold / ferroxidation / Iron | ||||||
Function / homology | Function and homology information oxidoreductase activity, acting on metal ions / ferric iron binding / DNA binding Similarity search - Function | ||||||
Biological species | Mycobacterium smegmatis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Direct refinement against model PDB / Resolution: 2.22 Å | ||||||
Authors | Williams, S.M. / Chandran, A.V. / Vijayabaskar, M.S. / Roy, S. / Balaram, H. / Vishveshwara, S. / Vijayan, M. / Chatterji, D. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2014 Title: A histidine aspartate ionic lock gates the iron passage in miniferritins from Mycobacterium smegmatis Authors: Williams, S.M. / Chandran, A.V. / Vijayabaskar, M.S. / Roy, S. / Balaram, H. / Vishveshwara, S. / Vijayan, M. / Chatterji, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4m33.cif.gz | 139.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4m33.ent.gz | 109.8 KB | Display | PDB format |
PDBx/mmJSON format | 4m33.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4m33_validation.pdf.gz | 453 KB | Display | wwPDB validaton report |
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Full document | 4m33_full_validation.pdf.gz | 455.3 KB | Display | |
Data in XML | 4m33_validation.xml.gz | 26.2 KB | Display | |
Data in CIF | 4m33_validation.cif.gz | 37.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m3/4m33 ftp://data.pdbj.org/pub/pdb/validation_reports/m3/4m33 | HTTPS FTP |
-Related structure data
Related structure data | 4m32C 4m34C 4m35C 2z90S C: citing same article (ref.) S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 18489.627 Da / Num. of mol.: 4 / Mutation: H141D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Strain: ATCC 700084 / mc(2)155 / Gene: DPS2, MSMEG_3242, MSMEI_3159 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0QXB7 #2: Chemical | ChemComp-FE2 / #3: Chemical | ChemComp-MG / #4: Chemical | #5: 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: 2.24 Å3/Da / Density % sol: 45.2 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS. |
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Crystal grow | Temperature: 298 K / Method: microbatch under oil / pH: 6.5 Details: 250mM MgCl2, 0.1M sodium cacodylate, 20% PEG3350, pH 6.5, Microbatch under oil, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54179 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 26, 2011 |
Radiation | Monochromator: Osmic / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54179 Å / Relative weight: 1 |
Reflection | Resolution: 2.21→30 Å / Num. obs: 33223 / Redundancy: 11.1 % / Biso Wilson estimate: 14.9 Å2 / Rmerge(I) obs: 0.134 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 2.21→2.33 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.328 / Mean I/σ(I) obs: 6.9 |
-Processing
Software |
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Refinement | Method to determine structure: Direct refinement against model PDB Starting model: 2z90 Resolution: 2.22→30 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.904 / SU B: 5.162 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R: 0.288 / ESU R Free: 0.199 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.774 Å2
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Refinement step | Cycle: LAST / Resolution: 2.22→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.22→2.278 Å / Total num. of bins used: 20
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