+Open data
-Basic information
Entry | Database: PDB / ID: 6hjh | ||||||
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Title | Myxococcus xanthus MglA bound to GDP | ||||||
Components | Mutual gliding-motility protein MglA | ||||||
Keywords | CYTOSOLIC PROTEIN / Small GTPase | ||||||
Function / homology | Function and homology information regulation of protein localization / GTPase activity / GTP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Myxococcus xanthus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å | ||||||
Authors | Varela, P.F. / Cherfils, J. | ||||||
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 | 6hjh.cif.gz | 92.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hjh.ent.gz | 70.8 KB | Display | PDB format |
PDBx/mmJSON format | 6hjh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hj/6hjh ftp://data.pdbj.org/pub/pdb/validation_reports/hj/6hjh | HTTPS FTP |
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-Related structure data
Related structure data | 6h17C 6h35C 6h5bC 6hjmC 6hjoC 3t1oS S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 22042.379 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Myxococcus xanthus (bacteria) / Gene: mglA, MXAN_1925 / Production host: Escherichia coli (E. coli) / References: UniProt: Q1DB04 |
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#2: Chemical | ChemComp-GDP / |
#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: 3.44 Å3/Da / Density % sol: 64.24 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: MES 0.1M, PEG 4000 30% |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 17, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9801 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→38.6 Å / Num. obs: 4841 / % possible obs: 47 % / Redundancy: 5.2 % / Biso Wilson estimate: 90.42 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.23 / Rrim(I) all: 0.26 / Net I/σ(I): 7.26 |
Reflection shell | Resolution: 3.3→3.4 Å / Redundancy: 5.4 % / Rmerge(I) obs: 1.6 / Num. unique obs: 135 / CC1/2: 0.4 / Rrim(I) all: 1.8 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3T1O Resolution: 3.3→38.6 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.789 / Rfactor Rfree error: 0 / Cross valid method: FREE R-VALUE / σ(F): 0 / SU Rfree Blow DPI: 1.104
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Displacement parameters | Biso mean: 103.94 Å2
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Refine analyze | Luzzati coordinate error obs: 0.42 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 3.3→38.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.3→3.69 Å / Rfactor Rfree error: 0 / Total num. of bins used: 5
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Refinement TLS params. | Method: refined / Origin x: 40.1012 Å / Origin y: -10.3245 Å / Origin z: 1.8733 Å
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Refinement TLS group | Selection details: { A|3 - A|192 } |