+Open data
-Basic information
Entry | Database: PDB / ID: 4asn | ||||||
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Title | TubR from Bacillus megaterium pBM400 | ||||||
Components | TUBRSanaa Governorate | ||||||
Keywords | TRANSCRIPTION / TUBULIN / FTSZ / SEGREGATION / PARTITION | ||||||
Function / homology | plasmid partitioning / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / DNA binding / Orthogonal Bundle / Mainly Alpha / DNA-binding protein TubR Function and homology information | ||||||
Biological species | BACILLUS MEGATERIUM (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.5 Å | ||||||
Authors | Aylett, C.H.S. / Lowe, J. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2012 Title: Superstructure of the Centromeric Complex of Tubzrc Plasmid Partitioning Systems. Authors: Aylett, C.H.S. / Lowe, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4asn.cif.gz | 61 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4asn.ent.gz | 50.3 KB | Display | PDB format |
PDBx/mmJSON format | 4asn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/as/4asn ftp://data.pdbj.org/pub/pdb/validation_reports/as/4asn | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 11700.768 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BACILLUS MEGATERIUM (bacteria) / Strain: QMB 1551 / Plasmid: PHIS17 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: Q848W2 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 5.11 Å3/Da / Density % sol: 75.94 % / Description: NONE |
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 8.5 Details: BM TUBR CRYSTALS WERE PRODUCED IN 500 NL TO 500 NL PROTEIN TO PRECIPITANT SITTING DROPS: 20 MG/ML BM TUBR, 100 MM TRIS-CL PH 8.5, 0.2 M SODIUM CITRATE, 15 % (V/V) PEG 400. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 14, 2011 |
Radiation | Monochromator: GRAPHITE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→46.09 Å / Num. obs: 17357 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 9.9 % / Biso Wilson estimate: 125.07 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 23.1 |
Reflection shell | Resolution: 3.5→3.69 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 4.8 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 3.5→46.085 Å / SU ML: 0.29 / σ(F): 1.27 / Phase error: 27.2 / Stereochemistry target values: ML / Details: SHARPENED -50 FOR SIDE CHAIN DENSITY.
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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: 144.55 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.5→46.085 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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