+Open data
-Basic information
Entry | Database: PDB / ID: 5g24 | ||||||
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Title | Type IV-like pilin TTHA1219 from Thermus thermophilus | ||||||
Components | TYPE-IV LIKE PILIN TTHA1219 | ||||||
Keywords | STRUCTURAL PROTEIN / NATURAL COMPETENCE / TYPE IV PILUS / DNA UPTAKE | ||||||
Function / homology | Prokaryotic N-terminal methylation site. / Prokaryotic N-terminal methylation site / cell outer membrane / Probable general secretion pathway protein J Function and homology information | ||||||
Biological species | THERMUS THERMOPHILUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Karuppiah, V. / Derrick, J.P. | ||||||
Citation | Journal: J.Struct.Biol. / Year: 2016 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5g24.cif.gz | 159.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5g24.ent.gz | 128 KB | Display | PDB format |
PDBx/mmJSON format | 5g24.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g2/5g24 ftp://data.pdbj.org/pub/pdb/validation_reports/g2/5g24 | HTTPS FTP |
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-Related structure data
Related structure data | 5g23SC 5g25C 5g2fC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.4715, 0.1321, 0.8719), Vector: |
-Components
#1: Protein | Mass: 25126.736 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / Production host: ESCHERICHIA COLI (E. coli) / Variant (production host): T7 EXPRESS / References: UniProt: Q5SIZ5 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 43 % / Description: NONE |
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Crystal grow | Details: 0.01M ZINC CHLORIDE, 0.1M SODIUM ACETATE PH 5 AND 20% (W/V) PEG 6000 |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→57.77 Å / Num. obs: 16586 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 8.1 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 2.3→2.36 Å / Redundancy: 8 % / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 2.6 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 5G23 Resolution: 2.3→97.58 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.922 / SU B: 17.194 / SU ML: 0.203 / Cross valid method: THROUGHOUT / ESU R: 0.403 / ESU R Free: 0.246 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.982 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→97.58 Å
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