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Yorodumi- PDB-7zpt: Crystal structure of MreB from Geobacillus stearothermophilus ATCC7953 -
+Open data
-Basic information
Entry | Database: PDB / ID: 7zpt | ||||||
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Title | Crystal structure of MreB from Geobacillus stearothermophilus ATCC7953 | ||||||
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 / Cell shape-determining protein MreB Function and homology information | ||||||
Biological species | Geobacillus stearothermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 | 7zpt.cif.gz | 95.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7zpt.ent.gz | 57 KB | Display | PDB format |
PDBx/mmJSON format | 7zpt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zp/7zpt ftp://data.pdbj.org/pub/pdb/validation_reports/zp/7zpt | HTTPS FTP |
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-Related structure data
Related structure data | 7zpuC 8azgC 4czjS 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: 36445.008 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus stearothermophilus (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-1PE / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.88 Å3/Da / Density % sol: 34.63 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.7 / Details: PEG 300, 2-(N-morpholino)ethanesulfonic acid |
-Data collection
Diffraction | Mean temperature: 100 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: 1.8→46.87 Å / Num. obs: 25002 / % possible obs: 99.5 % / Redundancy: 6.95 % / Biso Wilson estimate: 29.96 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.15 / Net I/σ(I): 7.21 |
Reflection shell | Resolution: 1.8→1.9 Å / Num. unique obs: 3960 / CC1/2: 0.76 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4CZJ Resolution: 1.8→46.87 Å / SU ML: 0.2221 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.1971 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: 32.99 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→46.87 Å
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Refine LS restraints |
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LS refinement shell |
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