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- PDB-2y4x: Structure of a domain from the type IV pilus biogenesis lipoprote... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2y4x | ||||||
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Title | Structure of a domain from the type IV pilus biogenesis lipoprotein PilP, from Pseudomonas aeruginosa PA01 | ||||||
![]() | PILP PROTEIN | ||||||
![]() | BIOSYNTHETIC PROTEIN | ||||||
Function / homology | ![]() type IV pilus / type IV pilus assembly / type IV pilus-dependent motility / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Derrick, J.P. / Berry, J. | ||||||
![]() | ![]() Title: Structure of a Domain from the Type Iv Pilus Biogenesis Lipoprotein Pilp Authors: Berry, J. / 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 | ![]() | 82.7 KB | Display | ![]() |
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PDB format | ![]() | 62.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 438.6 KB | Display | ![]() |
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Full document | ![]() | 444.6 KB | Display | |
Data in XML | ![]() | 10.6 KB | Display | |
Data in CIF | ![]() | 14 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2y4yS 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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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.757, 0.04987, 0.6515), Vector: |
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Components
#1: Protein | Mass: 10153.529 Da / Num. of mol.: 2 / Fragment: RESIDUES 83-171 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | Sequence details | GSHM SEQUENCE IS FROM THE EXPRESSION | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 42 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: 0.1M HEPES PH 7.5, 8% (V/V) ETHYLENE GLYCOL, 20% (W/V) PEG 10,000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU R-AXIS IV / Detector: IMAGE PLATE / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→30 Å / Num. obs: 16259 / % possible obs: 86.7 % / Observed criterion σ(I): 2.4 / Redundancy: 2.8 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.4 / % possible all: 85.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2Y4Y Resolution: 1.7→30 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.895 / SU B: 6.669 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.331 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.23 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→30 Å
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Refine LS restraints |
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