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Yorodumi- PDB-3nqr: A putative CBS domain-containing protein from Salmonella typhimur... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3nqr | ||||||
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Title | A putative CBS domain-containing protein from Salmonella typhimurium LT2 | ||||||
Components | Magnesium and cobalt efflux protein corC | ||||||
Keywords | TRANSPORT PROTEIN / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / CBS domain / efflux protein corC / Structure genomics | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Salmonella typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å | ||||||
Authors | Filippova, E.V. / Minasov, G. / Kiryukhina, O. / Shuvalova, L. / Cui, H. / Joachimiak, A. / Anderson, F.W. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: A putative CBS domain-containing protein from Salmonella typhimurium LT2. Authors: Filippova, E.V. / Minasov, G. / Kiryukhina, O. / Shuvalova, L. / Cui, H. / Joachimiak, A. / Anderson, F.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3nqr.cif.gz | 220.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3nqr.ent.gz | 179 KB | Display | PDB format |
PDBx/mmJSON format | 3nqr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nq/3nqr ftp://data.pdbj.org/pub/pdb/validation_reports/nq/3nqr | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 14878.149 Da / Num. of mol.: 4 / Fragment: CBS domain residues 65-191 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: corC, STM0667 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21magic / References: UniProt: P0A2L3 #2: Chemical | ChemComp-AMP / #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: 2.19 Å3/Da / Density % sol: 43.75 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1 M MES, 25% w/v PEG4000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 27, 2010 / Details: MIRROR |
Radiation | Monochromator: SI-111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 34373 / Num. obs: 34373 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 32.6 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 18.72 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.08 / % possible all: 97.7 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.911 / SU B: 9.874 / SU ML: 0.125 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.203 / ESU R Free: 0.191 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 22.581 Å2
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Refine analyze | Luzzati coordinate error obs: 0.25 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.001→2.053 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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