+Open data
-Basic information
Entry | Database: PDB / ID: 7ysz | ||||||
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Title | Spiroplasma melliferum FtsZ bound to GDP | ||||||
Components | Cell division protein FtsZ | ||||||
Keywords | CELL CYCLE / FtsZ / GTP binding / GTPase / cytoskeletal / tubulin homolog | ||||||
Function / homology | GUANOSINE-5'-DIPHOSPHATE / : Function and homology information | ||||||
Biological species | Spiroplasma melliferum KC3 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.30004123971 Å | ||||||
Authors | Chakraborty, J. / Pananghat, G. | ||||||
Funding support | India, 1items
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Citation | Journal: To Be Published Title: Structural basis of kinetic polarity of FtsZ from a cell wall less bacterium Spiroplasma Authors: Chakraborty, J. / Pananghat, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ysz.cif.gz | 150.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ysz.ent.gz | 93.7 KB | Display | PDB format |
PDBx/mmJSON format | 7ysz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ysz_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7ysz_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7ysz_validation.xml.gz | 24.5 KB | Display | |
Data in CIF | 7ysz_validation.cif.gz | 34.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ys/7ysz ftp://data.pdbj.org/pub/pdb/validation_reports/ys/7ysz | HTTPS FTP |
-Related structure data
Related structure data | 2vxyS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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
#1: Protein | Mass: 33630.055 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Spiroplasma melliferum KC3 (bacteria) / Gene: ftsZ, SPM_000165 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 AI / References: UniProt: A0A037UPJ1 #2: Chemical | #3: Chemical | ChemComp-TRS / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.69 Å3/Da / Density % sol: 58.87 % / Description: Needle-like crystals |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 1.5M ammonium sulphate, 0.1M Tris pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97623 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 10, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97623 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→49.1606915571 Å / Num. obs: 33121 / % possible obs: 99.7 % / Redundancy: 8.7 % / Biso Wilson estimate: 41.7708032157 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.088 / Net I/σ(I): 14.9 |
Reflection shell | Resolution: 2.3→2.38 Å / Rmerge(I) obs: 0.691 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 3217 / CC1/2: 0.808 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2VXY Resolution: 2.30004123971→49.1606915571 Å / SU ML: 0.242383543955 / Cross valid method: FREE R-VALUE / σ(F): 1.36521938216 / Phase error: 23.7456102644 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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: 50.9619401453 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.30004123971→49.1606915571 Å
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Refine LS restraints |
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LS refinement shell |
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