+Open data
-Basic information
Entry | Database: PDB / ID: 7cy1 | ||||||
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Title | Crystal Structure of MglC from Myxococcus xanthus | ||||||
Components | Mutual gliding motility protein C | ||||||
Keywords | CYTOSOLIC PROTEIN / Roadblock/LC7 domain | ||||||
Function / homology | GTPase Function and homology information | ||||||
Biological species | Myxococcus xanthus DK 1622 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å | ||||||
Authors | Thakur, K.G. / Kapoor, S. / Kodesia, A. | ||||||
Funding support | India, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2021 Title: Structural characterization of Myxococcus xanthus MglC, a component of the polarity control system, and its interactions with its paralog MglB. Authors: Kapoor, S. / Kodesia, A. / Kalidas, N. / Thakur, K.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7cy1.cif.gz | 38.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7cy1.ent.gz | 24.5 KB | Display | PDB format |
PDBx/mmJSON format | 7cy1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7cy1_validation.pdf.gz | 422.1 KB | Display | wwPDB validaton report |
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Full document | 7cy1_full_validation.pdf.gz | 423.5 KB | Display | |
Data in XML | 7cy1_validation.xml.gz | 7.1 KB | Display | |
Data in CIF | 7cy1_validation.cif.gz | 8.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cy/7cy1 ftp://data.pdbj.org/pub/pdb/validation_reports/cy/7cy1 | HTTPS FTP |
-Related structure data
Related structure data | 7ct3SC 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: 13134.907 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Myxococcus xanthus DK 1622 (bacteria) / Strain: DK 1622 / Gene: MXAN_5770 / Production host: Escherichia coli (E. coli) / References: UniProt: Q1D0B6 |
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#2: Chemical | ChemComp-NA / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.91 Å3/Da / Density % sol: 57.82 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2.8 M Sodium Acetate Trihydrate pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 0.98 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 26, 2020 / Details: LN2 closed loop cooling | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 2.19→27.98 Å / Num. obs: 8534 / % possible obs: 98.8 % / Redundancy: 18.1 % / CC1/2: 1 / Rmerge(I) obs: 0.075 / Net I/σ(I): 26.1 / Num. measured all: 154682 / Scaling rejects: 292 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7CT3 Resolution: 2.19→27.98 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.95 / SU B: 5.911 / SU ML: 0.144 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.202 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 142.17 Å2 / Biso mean: 46.966 Å2 / Biso min: 28.34 Å2
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Refinement step | Cycle: final / Resolution: 2.19→27.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.192→2.249 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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