+Open data
-Basic information
Entry | Database: PDB / ID: 6izw | |||||||||
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Title | Myxococcus xanthus MglA bound to GTP-gamma-S and MglB | |||||||||
Components |
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Keywords | SIGNALING PROTEIN / Small Ras-like GTPase / Cytosolic / Myxococcus motility protein / spatial oscillation | |||||||||
Function / homology | Function and homology information positive regulation of TOR signaling / guanyl-nucleotide exchange factor activity / regulation of protein localization / molecular adaptor activity / GTPase activity / GTP binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Myxococcus xanthus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | |||||||||
Authors | Baranwal, J. / Gayathri, P. | |||||||||
Funding support | India, 2items
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Citation | Journal: Plos Biol. / Year: 2019 Title: Allosteric regulation of a prokaryotic small Ras-like GTPase contributes to cell polarity oscillations in bacterial motility. Authors: Baranwal, J. / Lhospice, S. / Kanade, M. / Chakraborty, S. / Gade, P.R. / Harne, S. / Herrou, J. / Mignot, T. / Gayathri, P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6izw.cif.gz | 109.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6izw.ent.gz | 81.3 KB | Display | PDB format |
PDBx/mmJSON format | 6izw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6izw_validation.pdf.gz | 818.7 KB | Display | wwPDB validaton report |
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Full document | 6izw_full_validation.pdf.gz | 826.5 KB | Display | |
Data in XML | 6izw_validation.xml.gz | 20.8 KB | Display | |
Data in CIF | 6izw_validation.cif.gz | 29 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iz/6izw ftp://data.pdbj.org/pub/pdb/validation_reports/iz/6izw | HTTPS FTP |
-Related structure data
Related structure data | 5ymxC 3t12S 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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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 2 types, 3 molecules ABC
#1: Protein | Mass: 23015.391 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Myxococcus xanthus (strain DK 1622) (bacteria) Strain: DK 1622 / Gene: mglA, MXAN_1925 / Plasmid: pHis17 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q1DB04, small monomeric GTPase |
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#2: Protein | Mass: 18435.006 Da / Num. of mol.: 2 / Mutation: I148M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Myxococcus xanthus (strain DK 1622) (bacteria) Strain: DK 1622 / Gene: mglB, MXAN_1926 / Plasmid: pHis17 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21-AI / References: UniProt: Q1DB03 |
-Non-polymers , 4 types, 166 molecules
#3: Chemical | ChemComp-GSP / | ||
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#4: Chemical | ChemComp-MG / | ||
#5: Chemical | #6: 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: 2.56 Å3/Da / Density % sol: 52 % / Description: hexagonal, rod-shaped |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / Details: 8% PEG 4000, 200mM Ammonium sulphate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97915 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 15, 2017 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→44.241 Å / Num. obs: 23862 / % possible obs: 100 % / Redundancy: 9.8 % / Biso Wilson estimate: 42.7 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.044 / Rrim(I) all: 0.103 / Rsym value: 0.1 / Net I/σ(I): 16.5 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 9.9 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 2456 / CC1/2: 0.792 / Rpim(I) all: 0.358 / Rrim(I) all: 0.799 / Rsym value: 0.8 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3T12 Resolution: 2.4→44.241 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.23
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→44.241 Å
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Refine LS restraints |
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LS refinement shell |
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