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Yorodumi- PDB-3ent: Crystal structure of Nitrollin, a betagamma-crystallin from Nitro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ent | ||||||
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Title | Crystal structure of Nitrollin, a betagamma-crystallin from Nitrosospira multiformis-in alternate space group (P65) | ||||||
Components | Putative uncharacterized protein | ||||||
Keywords | STRUCTURAL PROTEIN / betagamma crystallin | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Nitrosospira multiformis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.14 Å | ||||||
Authors | Aravind, P. / Sankaranarayanan, R. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2009 Title: Three-dimensional domain swapping in nitrollin, a single-domain betagamma-crystallin from Nitrosospira multiformis, controls protein conformation and stability but not dimerization Authors: Aravind, P. / Suman, S.K. / Mishra, A. / Sharma, Y. / Sankaranarayanan, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ent.cif.gz | 58.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ent.ent.gz | 45.9 KB | Display | PDB format |
PDBx/mmJSON format | 3ent.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/en/3ent ftp://data.pdbj.org/pub/pdb/validation_reports/en/3ent | 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: 13325.176 Da / Num. of mol.: 2 Fragment: single domain betagamma-crystallin, residues 24-140 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nitrosospira multiformis (bacteria) / Strain: ATCC 25196 / Gene: 3786576 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2YAE2 #2: 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: 2.98 Å3/Da / Density % sol: 58.78 % / Mosaicity: 0.443 ° |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 26% PEG3350, 0.2M NaCl, 0.1M Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR 345dtb / Detector: IMAGE PLATE / Date: Oct 28, 2007 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.14→25 Å / Num. obs: 16884 / % possible obs: 98.1 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.056 / Χ2: 0.765 / Net I/σ(I): 26.659 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.14→25 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.828 / σ(F): 0
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Solvent computation | Bsol: 49.319 Å2 | ||||||||||||||||||||||||
Displacement parameters | Biso max: 73.58 Å2 / Biso mean: 39.682 Å2 / Biso min: 21.9 Å2
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Refinement step | Cycle: LAST / Resolution: 2.14→25 Å
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Refine LS restraints |
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Xplor file |
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