+Open data
-Basic information
Entry | Database: PDB / ID: 6ym9 | |||||||||
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Title | Mycobacterium tuberculosis FtsZ in complex with GTP-gamma-S | |||||||||
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 | Mycobacterium tuberculosis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å | |||||||||
Authors | Alnami, A.T. / Norton, R.S. / Pena, H.P. / Haider, M. / kozielski, F. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2021 Title: Conformational Flexibility of A Highly Conserved Helix Controls Cryptic Pocket Formation in FtsZ. Authors: Alnami, A. / Norton, R.S. / Pena, H.P. / Haider, S. / Kozielski, F. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ym9.cif.gz | 293.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ym9.ent.gz | 196.7 KB | Display | PDB format |
PDBx/mmJSON format | 6ym9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ym/6ym9 ftp://data.pdbj.org/pub/pdb/validation_reports/ym/6ym9 | HTTPS FTP |
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-Related structure data
Related structure data | 6y1uC 6y1vC 6ym1C 1rq7S 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: 32170.344 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh) (bacteria) Strain: CDC 1551 / Oshkosh / Gene: ftsZ, MT2209 / Production host: Escherichia coli (E. coli) / References: UniProt: P9WN94 #2: Chemical | ChemComp-GSP / | #3: 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: 3.15 Å3/Da / Density % sol: 60.96 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion / pH: 5.6 Details: 27.5% PEG4000, 0.4 M ammonium acetate and 0.1 M Na citrate, soaked with 10 mM GPS for 4 hr. |
-Data collection
Diffraction | Mean temperature: 86 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jul 20, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.03→181.33 Å / Num. obs: 51881 / % possible obs: 99 % / Redundancy: 5.7 % / Biso Wilson estimate: 37 Å2 / CC1/2: 0.998 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 2.03→2.14 Å / Num. unique obs: 7482 / CC1/2: 0.565 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1RQ7 Resolution: 2.03→77.13 Å / SU ML: 0.2512 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.9447 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: 44.49 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.03→77.13 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -49.623813722 Å / Origin y: 20.8060315026 Å / Origin z: 12.0076174702 Å
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Refinement TLS group | Selection details: all |