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Yorodumi- PDB-6h35: Myxococcus xanthus MglA bound to GDP and Pi with mixed inactive a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6h35 | ||||||
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Title | Myxococcus xanthus MglA bound to GDP and Pi with mixed inactive and active switch region conformations | ||||||
Components | Mutual gliding-motility protein MglA | ||||||
Keywords | CYTOSOLIC PROTEIN / small GTPase in a mixed state | ||||||
Function / homology | Function and homology information regulation of protein localization / GTPase activity / GTP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Myxococcus xanthus DK 1622 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Varela, P.F. / Galicia, C. / Cherfils, J. | ||||||
Funding support | France, 1items
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Citation | Journal: Nat Commun / Year: 2019 Title: MglA functions as a three-state GTPase to control movement reversals of Myxococcus xanthus. Authors: Galicia, C. / Lhospice, S. / Varela, P.F. / Trapani, S. / Zhang, W. / Navaza, J. / Herrou, J. / Mignot, T. / Cherfils, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6h35.cif.gz | 211.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6h35.ent.gz | 143 KB | Display | PDB format |
PDBx/mmJSON format | 6h35.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6h35_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6h35_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6h35_validation.xml.gz | 19 KB | Display | |
Data in CIF | 6h35_validation.cif.gz | 25.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h3/6h35 ftp://data.pdbj.org/pub/pdb/validation_reports/h3/6h35 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 22871.262 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Small GTPase / Source: (gene. exp.) Myxococcus xanthus DK 1622 (bacteria) / Gene: mglA, MXAN_1925 / Production host: Escherichia coli (E. coli) / References: UniProt: Q1DB04 #2: Chemical | #3: Chemical | ChemComp-PO4 / | #4: Chemical | ChemComp-MPD / ( #5: 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: 2.77 Å3/Da / Density % sol: 55.66 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M HEPES pH 7.5, 70% MPD |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 25, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98011 Å / Relative weight: 1 |
Reflection | Resolution: 2.299→50 Å / Num. obs: 93193 / % possible obs: 74.71 % / Redundancy: 5.3 % / Biso Wilson estimate: 38.07 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.16 / Rpim(I) all: 0.076 / Net I/σ(I): 8.29 |
Reflection shell | Resolution: 2.299→2.38 Å / Mean I/σ(I) obs: 1.03 / Num. unique obs: 474 / CC1/2: 0.392 / % possible all: 20.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→49.11 Å / SU ML: 0.2609 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.9156 / Stereochemistry target values: GeoStd + Monomer Library
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.8 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→49.11 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 32.303813486 Å / Origin y: 14.7277344099 Å / Origin z: 70.125826273 Å
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Refinement TLS group | Selection details: all |