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- PDB-3cnr: Crystal Structure of PilZ (XAC1133) from Xanthomonas axonopodis p... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3cnr | ||||||
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Title | Crystal Structure of PilZ (XAC1133) from Xanthomonas axonopodis pv citri | ||||||
![]() | Type IV fimbriae assembly protein | ||||||
![]() | UNKNOWN FUNCTION / PilZ / Xanthomonas citri / Type IV pilus assembly | ||||||
Function / homology | predicted glycosyltransferase like domains / PilZ domain / PilZ domain / cyclic-di-GMP binding / Thrombin, subunit H / Beta Barrel / Mainly Beta / Type IV fimbriae assembly protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Guzzo, C.R. / Farah, C.S. | ||||||
![]() | ![]() Title: PILZ protein structure and interactions with PILB and the FIMX EAL domain: implications for control of type IV pilus biogenesis. Authors: Guzzo, C.R. / Salinas, R.K. / Andrade, M.O. / Farah, C.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 46.6 KB | Display | ![]() |
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PDB format | ![]() | 37.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 411.9 KB | Display | ![]() |
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Full document | ![]() | 414.6 KB | Display | |
Data in XML | ![]() | 6.2 KB | Display | |
Data in CIF | ![]() | 9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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 domain:
NCS domain segments: Ens-ID: 1 / End label comp-ID: ALA / Refine code: 2
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Components
#1: Protein | Mass: 12677.885 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: 306 / Gene: pilZ / Plasmid: pET3a / Production host: ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 33.8 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 24% PEG 4000, 0.1 M Tris-HCl, 0.2 M magnesium chloride, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 1, 2007 | ||||||||||||
Radiation | Monochromator: Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.85→40 Å / Num. obs: 13687 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.7 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 24.7 | ||||||||||||
Reflection shell | Resolution: 1.85→1.92 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.601 / Mean I/σ(I) obs: 1.74 / % possible all: 92.1 |
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Processing
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Refinement | Method to determine structure: ![]() Details: Tyrosine 22 in both chains A and B do not present electron density for the side chain hydroxyl group. The occupancy of these OH groups were therefore set to zero. Tyrosine codons for this ...Details: Tyrosine 22 in both chains A and B do not present electron density for the side chain hydroxyl group. The occupancy of these OH groups were therefore set to zero. Tyrosine codons for this position were confirmed by sequencing.
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.861 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→35 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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