+Open data
-Basic information
Entry | Database: PDB / ID: 2o6f | ||||||
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Title | Structure of metal- free rTp34 from Treponema pallidum | ||||||
Components | 34 kDa membrane antigen | ||||||
Keywords | MEMBRANE PROTEIN / PROTEIN BINDING / Ig-fold / syphilis / metal-ion binding / dimer | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Treponema pallidum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.63 Å | ||||||
Authors | Machius, M. / Brautigam, C.A. / Deka, R.K. / Tomchick, D.R. / Lumpkins, S.B. / Norgard, M.V. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2007 Title: Crystal structure of the Tp34 (TP0971) lipoprotein of treponema pallidum: implications of its metal-bound state and affinity for human lactoferrin. Authors: Deka, R.K. / Brautigam, C.A. / Tomson, F.L. / Lumpkins, S.B. / Tomchick, D.R. / Machius, M. / 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 | 2o6f.cif.gz | 83.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2o6f.ent.gz | 63 KB | Display | PDB format |
PDBx/mmJSON format | 2o6f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2o6f_validation.pdf.gz | 462.3 KB | Display | wwPDB validaton report |
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Full document | 2o6f_full_validation.pdf.gz | 465.2 KB | Display | |
Data in XML | 2o6f_validation.xml.gz | 16.7 KB | Display | |
Data in CIF | 2o6f_validation.cif.gz | 24.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o6/2o6f ftp://data.pdbj.org/pub/pdb/validation_reports/o6/2o6f | HTTPS FTP |
-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: 20443.449 Da / Num. of mol.: 2 / Mutation: V16G, F17A, S18M, A19G, C20S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Treponema pallidum (bacteria) / Gene: tpd / Plasmid: pProExHTa / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-Blue / References: UniProt: P19478 #2: Chemical | #3: Chemical | #4: Chemical | #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: 2.09 Å3/Da / Density % sol: 41.06 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 2.4 M Ammonium sulfate, 0.1 M Bicine, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97899 Å |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Jul 14, 2006 |
Radiation | Monochromator: Double-crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97899 Å / Relative weight: 1 |
Reflection | Resolution: 1.63→26.03 Å / Num. all: 41967 / Num. obs: 41967 / % possible obs: 95.3 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 25 Å2 / Rsym value: 0.038 / Net I/σ(I): 32 |
Reflection shell | Resolution: 1.63→1.66 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 2016 / Rsym value: 0.487 / % possible all: 94.1 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: native protein Resolution: 1.63→26.03 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.8 / SU ML: 0.067 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.099 / ESU R Free: 0.097 / 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: 25.686 Å2
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Refine analyze | Luzzati coordinate error obs: 0.231 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.63→26.03 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.63→1.669 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 | Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth seq-ID: 29 - 185 / Label seq-ID: 33 - 189
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