+Open data
-Basic information
Entry | Database: PDB / ID: 3k8g | ||||||
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Title | Structure of crystal form I of TP0453 | ||||||
Components | 30kLP | ||||||
Keywords | MEMBRANE PROTEIN / Treponema pallidum / outmer membrane protein | ||||||
Function / homology | : / Outer membrane-associated lipoprotein TP0453 / cell outer membrane / Prokaryotic membrane lipoprotein lipid attachment site profile. / Outer membrane protein TP0453 Function and homology information | ||||||
Biological species | Treponema pallidum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Zhu, G. / Luthra, A. / Desrosiers, D. / Koszelak-Rosenblum, M. / Mulay, V. / Radolf, J.D. / Malkowski, M.G. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: The Transition from Closed to Open Conformation of Treponema pallidum Outer Membrane-associated Lipoprotein TP0453 Involves Membrane Sensing and Integration by Two Amphipathic Helices. Authors: Luthra, A. / Zhu, G. / Desrosiers, D.C. / Eggers, C.H. / Mulay, V. / Anand, A. / McArthur, F.A. / Romano, F.B. / Caimano, M.J. / Heuck, A.P. / Malkowski, M.G. / Radolf, J.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3k8g.cif.gz | 114 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3k8g.ent.gz | 87.8 KB | Display | PDB format |
PDBx/mmJSON format | 3k8g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3k8g_validation.pdf.gz | 457.7 KB | Display | wwPDB validaton report |
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Full document | 3k8g_full_validation.pdf.gz | 471 KB | Display | |
Data in XML | 3k8g_validation.xml.gz | 22.8 KB | Display | |
Data in CIF | 3k8g_validation.cif.gz | 32 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k8/3k8g ftp://data.pdbj.org/pub/pdb/validation_reports/k8/3k8g | HTTPS FTP |
-Related structure data
Related structure data | 3k8hC 3k8iC 3k8jSC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-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: 29147.111 Da / Num. of mol.: 2 / Fragment: residues 27-287 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Treponema pallidum (bacteria) / Gene: 30klp, TP_0453 / Plasmid: pET43.1a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O67998 #2: Chemical | ChemComp-MPD / ( #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: 2.68 Å3/Da / Density % sol: 54.08 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 12% PEG 3350, 0.1M MgCl2, 0.1M MES, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9789 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 3, 2008 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9789 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→50 Å / Num. all: 46264 / Num. obs: 46264 / % possible obs: 99.9 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 23.3 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.455 / Mean I/σ(I) obs: 3.4 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3K8J Resolution: 1.95→39.72 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.933 / SU B: 7.346 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.166 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 30.906 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→39.72 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.004 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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