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Open data
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Basic information
Entry | Database: PDB / ID: 3k8i | ||||||
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Title | Structure of crystal form IV of TP0453 | ||||||
![]() | 30kLP | ||||||
![]() | MEMBRANE PROTEIN / Treponema pallidum / outer membrane protein | ||||||
Function / homology | : / Outer membrane-associated lipoprotein TP0453 / cell outer membrane / Prokaryotic membrane lipoprotein lipid attachment site profile. / Outer membrane protein TP0453![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhu, G. / Luthra, A. / Desrosiers, D. / Koszelak-Rosenblum, M. / Mulay, V. / Radolf, J.D. / Malkowski, M.G. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 64.3 KB | Display | ![]() |
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PDB format | ![]() | 46.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 424.1 KB | Display | ![]() |
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Full document | ![]() | 429 KB | Display | |
Data in XML | ![]() | 11.7 KB | Display | |
Data in CIF | ![]() | 15.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3k8gC ![]() 3k8hC ![]() 3k8jSC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 29147.111 Da / Num. of mol.: 1 / Fragment: residues 27-287 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.81 % |
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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, 0.75% BOG, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 20, 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: 2.2→41.13 Å / Num. all: 14662 / Num. obs: 14662 / % possible obs: 98.8 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 29.6 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.191 / Mean I/σ(I) obs: 4.5 / % possible all: 89.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3K8J Resolution: 2.2→41.13 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.908 / SU B: 14.931 / SU ML: 0.172 / Cross valid method: THROUGHOUT / ESU R: 0.307 / ESU R Free: 0.234 / 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: 46.073 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→41.13 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.261 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -10.0803 Å / Origin y: 23.4963 Å / Origin z: -7.3591 Å
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