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Yorodumi- PDB-2y4y: Structure of a domain from the type IV pilus biogenesis lipoprote... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2y4y | ||||||
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Title | Structure of a domain from the type IV pilus biogenesis lipoprotein PilP, from Pseudomonas aeruginosa | ||||||
Components | PILP PROTEIN | ||||||
Keywords | BIOSYNTHETIC PROTEIN | ||||||
Function / homology | Function and homology information type IV pilus / type IV pilus assembly / type IV pilus-dependent motility / plasma membrane Similarity search - Function | ||||||
Biological species | PSEUDOMONAS AERUGINOSA PAO1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å | ||||||
Authors | Derrick, J.P. / Berry, J. | ||||||
Citation | Journal: To be Published Title: Structure of a Domain from the Type Iv Pilus Biogenesis Lipoprotein Pilp, from Pseudomonas Aeruginosa Authors: Berry, J. / 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 | 2y4y.cif.gz | 149.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2y4y.ent.gz | 118.2 KB | Display | PDB format |
PDBx/mmJSON format | 2y4y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y4/2y4y ftp://data.pdbj.org/pub/pdb/validation_reports/y4/2y4y | HTTPS FTP |
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-Related structure data
Related structure data | |
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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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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 10153.529 Da / Num. of mol.: 4 / Fragment: RESIDUES 83-171 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PSEUDOMONAS AERUGINOSA PAO1 (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q51354, UniProt: G3XCX7*PLUS #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-ACT / #4: Water | ChemComp-HOH / | Sequence details | GSHM IS FROM THE EXPRESSION | |
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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: 2.8 Å3/Da / Density % sol: 56 % / Description: NONE |
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Crystal grow | pH: 8.5 / Details: 0.1M TRIS-HCL PH 8.5, 0.6M ZINC ACETATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1.2822 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2822 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→32 Å / Num. obs: 47367 / % possible obs: 94.7 % / Observed criterion σ(I): 2 / Redundancy: 7.3 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 2.6 / % possible all: 92.6 |
-Processing
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Refinement | Method to determine structure: MAD Starting model: NONE Resolution: 1.7→32.22 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.929 / SU B: 3.782 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.097 / 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: 19.85 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→32.22 Å
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Refine LS restraints |
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