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Yorodumi- PDB-8azg: Crystal structure of MreB from Geobacillus stearothermophilus ATC... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8azg | ||||||
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Title | Crystal structure of MreB from Geobacillus stearothermophilus ATCC7953 in complex with ATP | ||||||
Components | Cell shape-determining protein MreB | ||||||
Keywords | STRUCTURAL PROTEIN / bacterial actin / bacterial cytoskeleton | ||||||
Function / homology | Cell shape determining protein MreB / MreB/Mbl protein / cell morphogenesis / ATPase, nucleotide binding domain / regulation of cell shape / ATP binding / cytoplasm / ADENOSINE-5'-TRIPHOSPHATE / Cell shape-determining protein MreB Function and homology information | ||||||
Biological species | Geobacillus stearothermophilus ATCC 7953 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å | ||||||
Authors | Li de la Sierra-Gallay, I. / Mao, W. | ||||||
Funding support | France, 1items
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Citation | Journal: Elife / Year: 2023 Title: On the role of nucleotides and lipids in the polymerization of the actin homolog MreB from a Gram-positive bacterium. Authors: Mao, W. / Renner, L.D. / Cornilleau, C. / Li de la Sierra-Gallay, I. / Afensiss, S. / Benlamara, S. / Ah-Seng, Y. / Van Tilbeurgh, H. / Nessler, S. / Bertin, A. / Chastanet, A. / Carballido-Lopez, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8azg.cif.gz | 96.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8azg.ent.gz | 56.8 KB | Display | PDB format |
PDBx/mmJSON format | 8azg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/az/8azg ftp://data.pdbj.org/pub/pdb/validation_reports/az/8azg | HTTPS FTP |
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-Related structure data
Related structure data | 7zptSC 7zpuC 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
#1: Protein | Mass: 37405.078 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus stearothermophilus ATCC 7953 (bacteria) Gene: mreB, B4109_2230, B4114_2117, GS458_2390 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A150MJ77 | ||||
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#2: Chemical | ChemComp-ATP / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.94 Å3/Da / Density % sol: 58.15 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: PEG 8000, glycerol, potassium phosphate, magnesium chloride |
-Data collection
Diffraction | Mean temperature: 95 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.978565 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 9, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978565 Å / Relative weight: 1 |
Reflection | Resolution: 2.29→43.88 Å / Num. obs: 19996 / % possible obs: 99.7 % / Redundancy: 13.13 % / Biso Wilson estimate: 48.1 Å2 / CC1/2: 1 / Rrim(I) all: 0.146 / Net I/σ(I): 12.41 |
Reflection shell | Resolution: 2.29→2.43 Å / Num. unique obs: 3130 / CC1/2: 0.84 / Rrim(I) all: 1.41 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7ZPT Resolution: 2.29→42.47 Å / SU ML: 0.2779 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.9527 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 58.48 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.29→42.47 Å
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Refine LS restraints |
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LS refinement shell |
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