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Yorodumi- PDB-6pnv: 1.42 Angstrom Resolution Crystal Structure of Translocation Prote... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6pnv | ||||||
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Title | 1.42 Angstrom Resolution Crystal Structure of Translocation Protein TolB from Salmonella enterica | ||||||
Components | Tol-Pal system protein TolB | ||||||
Keywords | TRANSLOCASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / translocation protein TolB. | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å | ||||||
Authors | Minasov, G. / Shuvalova, L. / Dubrovska, I. / Kiryukhina, O. / Endres, M. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: To Be Published Title: 1.42 Angstrom Resolution Crystal Structure of Translocation Protein TolB from Salmonella enterica Authors: Minasov, G. / Shuvalova, L. / Dubrovska, I. / Kiryukhina, O. / Endres, M. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6pnv.cif.gz | 196.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6pnv.ent.gz | 153.6 KB | Display | PDB format |
PDBx/mmJSON format | 6pnv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pn/6pnv ftp://data.pdbj.org/pub/pdb/validation_reports/pn/6pnv | HTTPS FTP |
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-Related structure data
Related structure data | 2w8bS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 43972.816 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) Strain: LT2-4 / Variant: enterica / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 / Variant (production host): Gold(DE3) / References: UniProt: A0A0D6H0D6, UniProt: Q8ZQT5*PLUS |
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#2: Chemical | ChemComp-K / |
#3: Chemical | ChemComp-NA / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.45 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Protein: 5.2 mg/ml, 0.01M Tris HCl (pH 8.3); Screen: PACT (G4), 0.2 M Potassium thiocyanate, 0.1 M Bis Tris propane pH 7.5, 20% (w/v) PEG 3350. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 19, 2019 / Details: C(111) |
Radiation | Monochromator: Be / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 1.42→30 Å / Num. obs: 67628 / % possible obs: 96.2 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 13.6 Å2 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.029 / Rrim(I) all: 0.062 / Rsym value: 0.054 / Χ2: 1.039 / Net I/σ(I): 22.8 |
Reflection shell | Resolution: 1.42→1.44 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.622 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3512 / CC1/2: 0.709 / Rpim(I) all: 0.368 / Rrim(I) all: 0.726 / Rsym value: 0.622 / Χ2: 1.034 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2w8b Resolution: 1.42→29.7 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.719 / SU ML: 0.047 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.083 / ESU R Free: 0.069 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 56.78 Å2 / Biso mean: 16.254 Å2 / Biso min: 6.79 Å2
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Refinement step | Cycle: final / Resolution: 1.42→29.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.42→1.457 Å / Rfactor Rfree error: 0 / 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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