+Open data
-Basic information
Entry | Database: PDB / ID: 3t1r | ||||||
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Title | MglB with tetrameric arrangement | ||||||
Components | Gliding protein MglB | ||||||
Keywords | SIGNALING PROTEIN / homodimer / GTPase activating protein / Bacterial Polarity and Motility / alpha/beta protein / signalling protein / catalytic GAP domain | ||||||
Function / homology | Function and homology information positive regulation of TOR signaling / guanyl-nucleotide exchange factor activity / cellular response to amino acid stimulus / molecular adaptor activity / identical protein binding / metal ion binding Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Miertzschke, M. / Vetter, I.R. / Koerner, C. / Wittinghofer, A. | ||||||
Citation | Journal: Embo J. / Year: 2011 Title: Structural analysis of the Ras-like G protein MglA and its cognate GAP MglB and implications for bacterial polarity. Authors: Miertzschke, M. / Koerner, C. / Vetter, I.R. / Keilberg, D. / Hot, E. / Leonardy, S. / Sogaard-Andersen, L. / Wittinghofer, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3t1r.cif.gz | 123.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3t1r.ent.gz | 96.1 KB | Display | PDB format |
PDBx/mmJSON format | 3t1r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3t1r_validation.pdf.gz | 458.2 KB | Display | wwPDB validaton report |
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Full document | 3t1r_full_validation.pdf.gz | 468.9 KB | Display | |
Data in XML | 3t1r_validation.xml.gz | 24.4 KB | Display | |
Data in CIF | 3t1r_validation.cif.gz | 34.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t1/3t1r ftp://data.pdbj.org/pub/pdb/validation_reports/t1/3t1r | HTTPS FTP |
-Related structure data
Related structure data | 3t12C 3t1oC 3t1qC 3t1sC 3t1tC 3t1vC 3t1xC 1j3wS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 17970.496 Da / Num. of mol.: 4 / Mutation: G65S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: TTHA1131 / Plasmid: pGexET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Codon Plus RIL / References: UniProt: Q5SJ83 #2: Chemical | ChemComp-MG / #3: Water | ChemComp-HOH / | |
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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: 2.27 Å3/Da / Density % sol: 45.9 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.1M MgCl2, 2.5M NaCl, 0.1 M Tris-HCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97874 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 2, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97874 Å / Relative weight: 1 |
Reflection | Resolution: 2→45.33 Å / Num. all: 44566 / Num. obs: 43770 / % possible obs: 98.2 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 |
Reflection shell | Resolution: 2→2.1 Å / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1J3W Resolution: 2→45.33 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.928 / SU B: 3.712 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R Free: 0.157 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.966 Å2
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Refinement step | Cycle: LAST / Resolution: 2→45.33 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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