+Open data
-Basic information
Entry | Database: PDB / ID: 6yd6 | ||||||
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Title | SaFtsZ-UCM152 (comp.20) | ||||||
Components | Cell division protein FtsZ | ||||||
Keywords | CELL CYCLE / Cell division protein | ||||||
Function / homology | Function and homology information chloroplast fission / FtsZ-dependent cytokinesis / division septum assembly / cell division site / protein polymerization / GTPase activity / GTP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Fernandez-Tornero, C. / Ruiz, F.M. / Andreu, J.M. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2021 Title: Targeting the FtsZ Allosteric Binding Site with a Novel Fluorescence Polarization Screen, Cytological and Structural Approaches for Antibacterial Discovery. Authors: Huecas, S. / Araujo-Bazan, L. / Ruiz, F.M. / Ruiz-Avila, L.B. / Martinez, R.F. / Escobar-Pena, A. / Artola, M. / Vazquez-Villa, H. / Martin-Fontecha, M. / Fernandez-Tornero, C. / Lopez- ...Authors: Huecas, S. / Araujo-Bazan, L. / Ruiz, F.M. / Ruiz-Avila, L.B. / Martinez, R.F. / Escobar-Pena, A. / Artola, M. / Vazquez-Villa, H. / Martin-Fontecha, M. / Fernandez-Tornero, C. / Lopez-Rodriguez, M.L. / Andreu, J.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6yd6.cif.gz | 158.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6yd6.ent.gz | 102.6 KB | Display | PDB format |
PDBx/mmJSON format | 6yd6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yd/6yd6 ftp://data.pdbj.org/pub/pdb/validation_reports/yd/6yd6 | HTTPS FTP |
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-Related structure data
Related structure data | 6yd1C 6yd5C 3v0aS 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 31737.939 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: ftsZ / Production host: Escherichia coli (E. coli) / References: UniProt: P0A031 |
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-Non-polymers , 6 types, 207 molecules
#2: Chemical | ChemComp-GDP / |
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#3: Chemical | ChemComp-OMW / |
#4: Chemical | ChemComp-K / |
#5: Chemical | ChemComp-MB3 / |
#6: Chemical | ChemComp-EDO / |
#7: Water | ChemComp-HOH / |
-Details
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: 2.34 Å3/Da / Density % sol: 47.41 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 25% PEG5K MME, 10% EthGly, 0.2 M Li2SO4, 0.1 M Tris pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97918 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 17, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→40.16 Å / Num. obs: 31638 / % possible obs: 97.43 % / Redundancy: 3 % / Biso Wilson estimate: 23.65 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.03 / Rpim(I) all: 0.03 / Rrim(I) all: 0.04 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 1.7→1.77 Å / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 2.03 / Num. unique obs: 3192 / CC1/2: 0.82 / Rpim(I) all: 0.3 / Rrim(I) all: 0.43 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3V0A Resolution: 1.7→40.16 Å / SU ML: 0.2078 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.7786 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: 31.07 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→40.16 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A
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