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Yorodumi- PDB-5my5: Tungstate binding protein - TupA - from Desulfovibrio alaskensis G20 -
+Open data
-Basic information
Entry | Database: PDB / ID: 5my5 | ||||||||||||
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Title | Tungstate binding protein - TupA - from Desulfovibrio alaskensis G20 | ||||||||||||
Components | ABC transporter periplasmic substrate-binding protein | ||||||||||||
Keywords | TRANSPORT PROTEIN / susbtrate binding protein / TupA / tungstate / Desulfovibrio alaskensis G20 / ABC transporter / tungsten detection / sulphate reducing bacteria | ||||||||||||
Function / homology | PBP superfamily domain / PBP domain / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta / ABC transporter periplasmic substrate-binding protein Function and homology information | ||||||||||||
Biological species | Desulfovibrio alaskensis (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||||||||
Authors | Otrelo-Cardoso, A.R. / Correia, M.A.S.C. / Santos-Silva, T. | ||||||||||||
Funding support | Portugal, 3items
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Citation | Journal: Sci Rep / Year: 2017 Title: Highly selective tungstate transporter protein TupA from Desulfovibrio alaskensis G20. Authors: Otrelo-Cardoso, A.R. / Nair, R.R. / Correia, M.A.S. / Cordeiro, R.S.C. / Panjkovich, A. / Svergun, D.I. / Santos-Silva, T. / Rivas, M.G. #1: Journal: Int J Mol Sci / Year: 2014 Title: TupA: a tungstate binding protein in the periplasm of Desulfovibrio alaskensis G20. Authors: Otrelo-Cardoso, A.R. / Nair, R.R. / Correia, M.A.S. / Rivas, M.G. / Santos-Silva, T. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5my5.cif.gz | 71.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5my5.ent.gz | 50.4 KB | Display | PDB format |
PDBx/mmJSON format | 5my5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/my/5my5 ftp://data.pdbj.org/pub/pdb/validation_reports/my/5my5 | 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: 29697.885 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Desulfovibrio alaskensis (strain G20) (bacteria) Gene: Dde_0234 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q316W1 | ||
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#2: Chemical | ChemComp-NA / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.77 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop Details: 0.2 M magnesium chloride, 0.1 M HEPES (pH 7.5) and 30% (w/v) polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.954 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 13, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.954 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→42.53 Å / Num. obs: 46519 / % possible obs: 98.5 % / Redundancy: 2.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.034 / Rpim(I) all: 0.033 / Rrim(I) all: 0.048 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 1.4→1.42 Å / Rmerge(I) obs: 0.297 / Mean I/σ(I) obs: 2.4 / Num. unique all: 2277 / CC1/2: 0.903 / Rpim(I) all: 0.288 / Rrim(I) all: 0.414 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3LR1, 3MUQ Resolution: 1.4→42.53 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.722 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.063 / ESU R Free: 0.07 / 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: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.668 Å2
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Refinement step | Cycle: 1 / Resolution: 1.4→42.53 Å
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Refine LS restraints |
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