+Open data
-Basic information
Entry | Database: PDB / ID: 4xho | ||||||
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Title | Bacillus thuringiensis ParM with ATP | ||||||
Components | Uncharacterized protein | ||||||
Keywords | STRUCTURAL PROTEIN / BACTERIAL ACTIN-LIKE PROTEIN / BACTERIAL CYTOSKELETON | ||||||
Function / homology | Actin-like protein, N-terminal / Actin like proteins N terminal domain / ParM-like / ATPase, nucleotide binding domain / ATP binding / ADENOSINE-5'-TRIPHOSPHATE / : / ParM/StbA family protein Function and homology information | ||||||
Biological species | Bacillus thuringiensis serovar kurstaki (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.65 Å | ||||||
Authors | Jiang, S.M. / Robinson, R.C. | ||||||
Funding support | Singapore, 1items
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Citation | Journal: to be published Title: A novel plasmid-segregating actin-like protein from Bacillus thuringiensis forms dynamically unstable tubules Authors: Jiang, S.M. / Narita, A. / Popp, D. / Ghoshdastider, U. / Lee, L.J. / Srinivasan, R. / Balasubramanian, M.K. / Oda, T. / Koh, F.J. / Larsson, M. / Robinson, R.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4xho.cif.gz | 170.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xho.ent.gz | 133.4 KB | Display | PDB format |
PDBx/mmJSON format | 4xho.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4xho_validation.pdf.gz | 755.5 KB | Display | wwPDB validaton report |
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Full document | 4xho_full_validation.pdf.gz | 760.8 KB | Display | |
Data in XML | 4xho_validation.xml.gz | 17.4 KB | Display | |
Data in CIF | 4xho_validation.cif.gz | 24.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xh/4xho ftp://data.pdbj.org/pub/pdb/validation_reports/xh/4xho | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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Details | monomer |
-Components
#1: Protein | Mass: 47478.523 Da / Num. of mol.: 1 / Mutation: M356D/F360D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus thuringiensis serovar kurstaki (bacteria) Strain: YBT-1520 / Gene: YBT1520_33546 / Plasmid: pSY5, modified / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A024E1G1, UniProt: A0A0F6FJ34*PLUS |
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#2: Chemical | ChemComp-ATP / |
#3: Chemical | ChemComp-MG / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.71 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M Bis-Tris, pH 6.5, 0.2 M ammonium acetate, 25% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 10, 2008 / Details: Quantum-315 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.65→30 Å / Num. obs: 14327 / % possible obs: 100 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.057 / Χ2: 0.972 / Net I/av σ(I): 30.962 / Net I/σ(I): 15.4 / Num. measured all: 102248 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→28.825 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 27.23 / Stereochemistry target values: ML
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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 max: 132.05 Å2 / Biso mean: 36.5238 Å2 / Biso min: 7.45 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.65→28.825 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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Refinement TLS params. | Method: refined / Origin x: -47.1379 Å / Origin y: -55.4987 Å / Origin z: 235.4359 Å
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Refinement TLS group |
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