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Yorodumi- PDB-4a4y: Structure of the Cytosolic Domain of the Shigella T3SS component MxiG -
+Open data
-Basic information
Entry | Database: PDB / ID: 4a4y | ||||||
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Title | Structure of the Cytosolic Domain of the Shigella T3SS component MxiG | ||||||
Components | PROTEIN MXIG | ||||||
Keywords | PROTEIN BINDING / FHA DOMAIN | ||||||
Function / homology | Tumour Suppressor Smad4 - #50 / Type III secretion system, PrgH/EprH-like / Type III secretion system protein PrgH-EprH (PrgH) / Tumour Suppressor Smad4 / cell outer membrane / Sandwich / Mainly Beta / plasma membrane / Protein MxiG Function and homology information | ||||||
Biological species | SHIGELLA FLEXNERI (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å | ||||||
Authors | Barison, N. / Kolbe, M. | ||||||
Citation | Journal: Faseb J. / Year: 2012 Title: Interaction of Mxig with the Cytosolic Complex of the Type III Secretion System Controls Shigella Virulence. Authors: Barison, N. / Lambers, J. / Hurwitz, R. / Kolbe, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4a4y.cif.gz | 72 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4a4y.ent.gz | 55.3 KB | Display | PDB format |
PDBx/mmJSON format | 4a4y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4a4y_validation.pdf.gz | 439.8 KB | Display | wwPDB validaton report |
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Full document | 4a4y_full_validation.pdf.gz | 445.2 KB | Display | |
Data in XML | 4a4y_validation.xml.gz | 9.2 KB | Display | |
Data in CIF | 4a4y_validation.cif.gz | 11.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a4/4a4y ftp://data.pdbj.org/pub/pdb/validation_reports/a4/4a4y | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 16499.324 Da / Num. of mol.: 1 / Fragment: CYTOPLASMIC DOMAIN, RESIDUES 1-126 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SHIGELLA FLEXNERI (bacteria) / Strain: M90T / Variant: SEROTYPE 5A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A221 | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | N-TERMINAL HIS-TAG | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.57 % Description: SE-MET STRUCTURE SOLVED USING SOLVE-RESOLVE ANALYSIS OF 4 WAVELENGTH MAD: PEAK 0.97962 A, INFLECTION 0.97973 A, REMOTE (HIGH E) 0.97194 A, REMOTE (LOW E) 0.99535 A. |
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Crystal grow | Details: PROTEIN WAS CRYSTALLIZED FROM 0.085 M HEPES SODIUM PH 7.5, 1.7% POLYETHYLENE GLYCOL 400, 1.7 M AMMONIUM SULFATE, 15% GLYCEROL. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 1.071 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 16, 2010 / Details: MIRRORS |
Radiation | Monochromator: SI-111 CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.071 Å / Relative weight: 1 |
Reflection | Resolution: 1.57→41.04 Å / Num. obs: 23028 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 11 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 23.13 |
Reflection shell | Resolution: 1.57→1.61 Å / Redundancy: 8.9 % / Rmerge(I) obs: 1.1 / Mean I/σ(I) obs: 2.02 / % possible all: 98.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: STRUCTURE OF SE-MET DERIVATIVE Resolution: 1.57→41.05 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.961 / SU B: 3.64 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES RESIDUAL ONLY. RESIDUES 47-50 ARE DISORDERED
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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: 36.893 Å2
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Refinement step | Cycle: LAST / Resolution: 1.57→41.05 Å
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Refine LS restraints |
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