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Yorodumi- PDB-4foj: 1.55 A Crystal Structure of Xanthomonas citri FimX EAL domain in ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4foj | ||||||
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Title | 1.55 A Crystal Structure of Xanthomonas citri FimX EAL domain in complex with c-diGMP | ||||||
Components | FimX | ||||||
Keywords | PROTEIN BINDING / TIM like Barrel / beta-(beta/alpha)6-beta / c-di-GMP binding / Type IV pilus assembly / PilZ | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Xanthomonas axonopodis pv. citri (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Farah, C.S. / Guzzo, C.R. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2013 Title: Structure of the PilZ-FimXEAL-c-di-GMP Complex Responsible for the Regulation of Bacterial Type IV Pilus Biogenesis. Authors: Guzzo, C.R. / Dunger, G. / Salinas, R.K. / Farah, C.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4foj.cif.gz | 76.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4foj.ent.gz | 55.6 KB | Display | PDB format |
PDBx/mmJSON format | 4foj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fo/4foj ftp://data.pdbj.org/pub/pdb/validation_reports/fo/4foj | HTTPS FTP |
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-Related 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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-Components
#1: Protein | Mass: 29612.451 Da / Num. of mol.: 1 / Fragment: EAL domain (UNP residues 426-689) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xanthomonas axonopodis pv. citri (bacteria) Strain: 306 / Gene: XAC2398 / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q8PJX9 |
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#2: Chemical | ChemComp-C2E / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.7 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.7 Details: 0.6 M ammonium sulfate, 0.1 M sodium citrate, pH 4.7, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.24 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 24, 2011 |
Radiation | Monochromator: double flat crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.24 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→50 Å / Num. all: 50267 / Num. obs: 50267 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.8 % / Rsym value: 0.05 / Net I/σ(I): 38.45 |
Reflection shell | Resolution: 1.4→1.45 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 1.93 / Rsym value: 0.55 / % possible all: 68 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→30 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.942 / SU B: 1.608 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.089 / ESU R Free: 0.096 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.828 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.59 Å / Total num. of bins used: 20
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