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Open data
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Basic information
Entry | Database: PDB / ID: 7yop | ||||||
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Title | Spiroplasma melliferum FtsZ bound to GMPPNP | ||||||
![]() | Cell division protein FtsZ | ||||||
![]() | CELL CYCLE / FtsZ / GTP binding / GTPase / cytoskeletal / tubulin homolog | ||||||
Function / homology | GUANOSINE-5'-DIPHOSPHATE / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / : ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chakraborty, J. / Pananghat, G. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 158 KB | Display | ![]() |
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PDB format | ![]() | 98.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 26.8 KB | Display | |
Data in CIF | ![]() | 38.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2vxyS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() #2: Chemical | ChemComp-TRS / | #3: Chemical | ChemComp-GDP / | #4: Chemical | ChemComp-GNP / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.96 Å3/Da / Density % sol: 58.45 % / Description: Needle shape crystals |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop 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: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / 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: 2.2→49.2361734647 Å / Num. obs: 38294 / % possible obs: 99.5 % / Redundancy: 5.8 % / Biso Wilson estimate: 33.3678269305 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.031 / Rrim(I) all: 0.075 / Net I/σ(I): 17 |
Reflection shell | Resolution: 2.2→2.2 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 4.3 / Num. unique obs: 17906 / CC1/2: 0.894 / Rpim(I) all: 0.28 / Rrim(I) all: 0.485 / % possible all: 98.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2VXY Resolution: 2.20003123654→49.2361734647 Å / SU ML: 0.223321967793 / Cross valid method: FREE R-VALUE / σ(F): 1.37111906751 / Phase error: 22.6612563806 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: 43.6665595695 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.20003123654→49.2361734647 Å
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Refine LS restraints |
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LS refinement shell |
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