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Open data
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Basic information
Entry | Database: PDB / ID: 5g25 | ||||||
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Title | Type IV-like pilin TTHA1218 from Thermus thermophilus | ||||||
![]() | TYPE-IV LIKE COMPETENCE PILIN TTHA1218 | ||||||
![]() | STRUCTURAL PROTEIN / NATURAL COMPETENCE / TYPE IV PILUS / DNA UPTAKE | ||||||
Function / homology | Prokaryotic N-terminal methylation site. / Prokaryotic N-terminal methylation site / cell outer membrane / periplasmic space / Probable prepilin-like protein![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Karuppiah, V. / Derrick, J.P. | ||||||
![]() | ![]() Title: Structures of Type Iv Pilins from Thermus Thermophilus Demonstrate Similarities with Type II Secretion System Pseudopilins Authors: Karuppiah, V. / Thistlethwaite, A. / Derrick, J.P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 24.9 KB | Display | ![]() |
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PDB format | ![]() | 20.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 288.7 KB | Display | ![]() |
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Full document | ![]() | 288.6 KB | Display | |
Data in XML | ![]() | 5.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 10710.224 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-GOL / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.73 Å3/Da / Density % sol: 67.06 % / Description: NONE |
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Crystal grow | Details: 0.1 M HEPES PH 7.0 1M SUCCINIC ACID 1% PEG 2000 MME |
-Data collection
Diffraction |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 2.3→55.36 Å / Num. obs: 7765 / % possible obs: 99.9 % / Observed criterion σ(I): 3.6 / Redundancy: 11.6 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 30.1 | |||||||||||||||
Reflection shell | Resolution: 2.3→2.36 Å / Redundancy: 12.2 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 3.6 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: NONE Resolution: 2.3→90.41 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.942 / SU B: 4.483 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R: 0.177 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 56.233 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→90.41 Å
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Refine LS restraints |
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