+Open data
-Basic information
Entry | Database: PDB / ID: 5u2p | ||||||
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Title | The crystal structure of Tp0737 from Treponema pallidum | ||||||
Components | Sugar ABC transporter substrate-binding protein | ||||||
Keywords | TRANSPORT PROTEIN / ABC transporter / ligand-binding protein | ||||||
Function / homology | BROMIDE ION / : Function and homology information | ||||||
Biological species | Treponema pallidum subsp. pallidum (syphilis treponeme) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.76 Å | ||||||
Authors | Brautigam, C.A. / Deka, R.K. / Tomchick, D.R. / Norgard, M.V. | ||||||
Funding support | United States, 1items
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Citation | Journal: Protein Sci. / Year: 2017 Title: Functional clues from the crystal structure of an orphan periplasmic ligand-binding protein from Treponema pallidum. Authors: Brautigam, C.A. / Deka, R.K. / Liu, W.Z. / Tomchick, D.R. / Norgard, M.V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5u2p.cif.gz | 232 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5u2p.ent.gz | 189.2 KB | Display | PDB format |
PDBx/mmJSON format | 5u2p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5u2p_validation.pdf.gz | 439.3 KB | Display | wwPDB validaton report |
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Full document | 5u2p_full_validation.pdf.gz | 440.6 KB | Display | |
Data in XML | 5u2p_validation.xml.gz | 17.3 KB | Display | |
Data in CIF | 5u2p_validation.cif.gz | 25.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u2/5u2p ftp://data.pdbj.org/pub/pdb/validation_reports/u2/5u2p | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 47718.188 Da / Num. of mol.: 1 / Fragment: residues 28-436 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Treponema pallidum subsp. pallidum (syphilis treponeme) Gene: A8P32_03680 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1B3KAD9 | ||||
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#2: Chemical | ChemComp-BR / | ||||
#3: Chemical | #4: Chemical | ChemComp-EDO / | #5: 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: 2.25 Å3/Da / Density % sol: 45.35 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / Details: 0.2 M NaBr 0.1 M Bis-Tris Propane 20% PEK 3,350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 9, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 1.76→37.539 Å / Num. obs: 43052 / % possible obs: 97.4 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 19.6 |
Reflection shell | Resolution: 1.76→1.79 Å / Rmerge(I) obs: 0.365 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.76→37.539 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.95 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.76→37.539 Å
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Refine LS restraints |
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LS refinement shell |
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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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