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Yorodumi- PDB-4xhp: Bacillus thuringiensis ParM hybrid protein with ADP, containing t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4xhp | ||||||
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Title | Bacillus thuringiensis ParM hybrid protein with ADP, containing two ParM mutants | ||||||
Components | ParM hybrid fusion 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'-DIPHOSPHATE / : / ParM/StbA family protein Function and homology information | ||||||
Biological species | Bacillus thuringiensis serovar kurstaki str. YBT-1520 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.2 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 | 4xhp.cif.gz | 155.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xhp.ent.gz | 124.3 KB | Display | PDB format |
PDBx/mmJSON format | 4xhp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4xhp_validation.pdf.gz | 988 KB | Display | wwPDB validaton report |
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Full document | 4xhp_full_validation.pdf.gz | 1004.1 KB | Display | |
Data in XML | 4xhp_validation.xml.gz | 28.5 KB | Display | |
Data in CIF | 4xhp_validation.cif.gz | 38.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xh/4xhp ftp://data.pdbj.org/pub/pdb/validation_reports/xh/4xhp | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | monomer |
-Components
#1: Protein | Mass: 96398.508 Da / Num. of mol.: 1 / Mutation: F288D, M289D, P331D, M799D, F803D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus thuringiensis serovar kurstaki str. YBT-1520 (bacteria) 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 | #3: Chemical | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.25 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 0.1 M sodium acetate, pH 5.0, 5% poly-gamma-glutamic acid polymer, 30% PEG 400 |
-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: Mar 6, 2012 / 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: 3.2→30 Å / Num. obs: 15010 / % possible obs: 97.5 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.062 / Χ2: 0.877 / Net I/av σ(I): 15.972 / Net I/σ(I): 10.1 / Num. measured all: 46526 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→27.75 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 31.48 / 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: 201.99 Å2 / Biso mean: 63.2716 Å2 / Biso min: 30.62 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.2→27.75 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: 9
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