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- PDB-4m32: Crystal structure of gated-pore mutant D138N of second DNA-Bindin... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4m32 | ||||||
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Title | Crystal structure of gated-pore mutant D138N of second DNA-Binding protein under starvation from Mycobacterium smegmatis | ||||||
![]() | Putative starvation-induced DNA protecting protein/Ferritin and Dps | ||||||
![]() | DNA BINDING PROTEIN / ferritin-like fold / ferroxidation / Iron | ||||||
Function / homology | ![]() oxidoreductase activity, acting on metal ions / ferric iron binding / DNA binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() | ||||||
![]() | Williams, S.M. / Chandran, A.V. / Vijayabaskar, M.S. / Roy, S. / Balaram, H. / Vishveshwara, S. / Vijayan, M. / Chatterji, D. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 141.9 KB | Display | ![]() |
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PDB format | ![]() | 111.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 447.7 KB | Display | ![]() |
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Full document | ![]() | 450.8 KB | Display | |
Data in XML | ![]() | 27.1 KB | Display | |
Data in CIF | ![]() | 39.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4m33C ![]() 4m34C ![]() 4m35C ![]() 2z90S C: citing same article ( S: Starting model for refinement |
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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 on special symmetry positions |
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Components
#1: Protein | Mass: 18511.699 Da / Num. of mol.: 4 / Mutation: D138N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-FE2 / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.06 % 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: 150mM 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: ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 27, 2011 / Details: mirrors |
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: 1.85→43.57 Å / Num. obs: 55022 / Redundancy: 4.6 % / Biso Wilson estimate: 19.5 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 15.3 |
Reflection shell | Resolution: 1.85→1.95 Å / Redundancy: 5 % / Rmerge(I) obs: 0.232 / Mean I/σ(I) obs: 5.6 |
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Processing
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Refinement | Method to determine structure: Direct refinement against model PDB Starting model: 2z90 Resolution: 1.86→30 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.557 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.145 / ESU R Free: 0.127 / 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: 15.327 Å2
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Refinement step | Cycle: LAST / Resolution: 1.86→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.86→1.91 Å / Total num. of bins used: 20
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