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Yorodumi- PDB-4npa: Scrystal structure of protein with unknown function from Vibrio c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4npa | ||||||
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Title | Scrystal structure of protein with unknown function from Vibrio cholerae at P22121 spacegroup | ||||||
Components | Putative uncharacterized protein | ||||||
Keywords | UNKNOWN FUNCTION / STRUCTURAL GENOMICS | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Vibrio cholerae O1 biovar El Tor (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Boyko, K.M. / Gorbacheva, M.A. / Rakitina, T.V. / Korgenevsky, D.A. / Dorovatovsky, P.V. / Lipkin, A.V. / Minor, W. / Shumilin, I.A. / Popov, V.O. | ||||||
Citation | Journal: To be Published Title: Crystal structure of protein with unknown function from Vibrio cholerae at P22121 spacegroup Authors: Boyko, K.M. / Gorbacheva, M.A. / Rakitina, T.V. / Korgenevsky, D.A. / Dorovatovsky, P.V. / Lipkin, A.V. / Minor, W. / Shumilin, I.A. / Popov, V.O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4npa.cif.gz | 325.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4npa.ent.gz | 261 KB | Display | PDB format |
PDBx/mmJSON format | 4npa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/np/4npa ftp://data.pdbj.org/pub/pdb/validation_reports/np/4npa | HTTPS FTP |
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-Related structure data
Related structure data | 2pmbS 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
#1: Protein | Mass: 50893.254 Da / Num. of mol.: 4 / Fragment: UNP residues 7-457 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae O1 biovar El Tor (bacteria) Strain: ATCC 39315 / El Tor Inaba N16961 / Gene: VC_0899 / Plasmid: pET-24 / Production host: Escherichia coli (E. coli) / Strain (production host): LT2 / References: UniProt: Q9KTK3 #2: Chemical | ChemComp-SO4 / | #3: Chemical | #4: Chemical | ChemComp-PEG / | #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: 2.3 Å3/Da / Density % sol: 46.52 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 500mM NaCl, 10mM HEPES, 4%(v/v) Tacsimate, 18%(w/v) PEG3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.8 Å |
Detector | Type: MAR225HE / Detector: CCD / Date: Dec 24, 2010 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→30 Å / Num. all: 111393 / Num. obs: 111393 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 1.9 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2PMB Resolution: 2.1→29.74 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.909 / SU B: 5.807 / SU ML: 0.154 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.216 / ESU R Free: 0.199 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.972 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→29.74 Å
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Refine LS restraints |
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