+Open data
-Basic information
Entry | Database: PDB / ID: 8grw | ||||||
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Title | Spiroplasma melliferum FtsZ F224M bound to GDP | ||||||
Components | Cell division protein FtsZ | ||||||
Keywords | CELL CYCLE / FtsZ / 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: 2.40005414899 Å | ||||||
Authors | Chakraborty, J. / Pananghat, G. | ||||||
Funding support | 1items
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Citation | Journal: J.Biol.Chem. / Year: 2024 Title: Dynamics of interdomain rotation facilitates FtsZ filament assembly. Authors: Chakraborty, J. / Poddar, S. / Dutta, S. / Bahulekar, V. / Harne, S. / Srinivasan, R. / Gayathri, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8grw.cif.gz | 147 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8grw.ent.gz | 92.3 KB | Display | PDB format |
PDBx/mmJSON format | 8grw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8grw_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 8grw_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 8grw_validation.xml.gz | 23.3 KB | Display | |
Data in CIF | 8grw_validation.cif.gz | 32.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gr/8grw ftp://data.pdbj.org/pub/pdb/validation_reports/gr/8grw | HTTPS FTP |
-Related structure data
Related structure data | 7yopC 7yszSC S: Starting model for refinement C: citing same article (ref.) |
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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: 33614.074 Da / Num. of mol.: 2 / Mutation: F224M 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 | ChemComp-TRS / | #3: Chemical | #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: 2.72 Å3/Da / Density % sol: 59.28 % / Description: Needle shape crystal |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.3M sodium acetate, 0.1M Tris pH 8.5, 15% w/v PEG 4000 |
-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: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 24, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→106.67 Å / Num. obs: 29504 / % possible obs: 99.5 % / Redundancy: 7 % / Biso Wilson estimate: 38.6527126985 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.096 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 2.4→2.49 Å / Rmerge(I) obs: 0.684 / Num. unique obs: 3038 / CC1/2: 0.785 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7YSZ Resolution: 2.40005414899→49.2757806587 Å / SU ML: 0.270757548432 / Cross valid method: FREE R-VALUE / σ(F): 1.34748269832 / Phase error: 24.4056862686 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: 46.2142735292 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.40005414899→49.2757806587 Å
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Refine LS restraints |
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LS refinement shell |
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