+Open data
-Basic information
Entry | Database: PDB / ID: 4b6w | ||||||
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Title | Architecture of Trypanosoma brucei Tubulin-Binding cofactor B | ||||||
Components | TUBULIN-SPECIFIC CHAPERONE | ||||||
Keywords | CHAPERONE / CAP-GLY / UBIQUITIN-LIKE | ||||||
Function / homology | Function and homology information Ubiquitin-like domain / CAP Gly-rich domain / CAP Gly-rich domain superfamily / CAP-Gly domain / CAP-Gly domain profile. / CAP_GLY / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin-like domain / Ubiquitin-like domain superfamily ...Ubiquitin-like domain / CAP Gly-rich domain / CAP Gly-rich domain superfamily / CAP-Gly domain / CAP-Gly domain profile. / CAP_GLY / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | TRYPANOSOMA BRUCEI BRUCEI STRAIN 927/4 GUTAT10.1 (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.35 Å | ||||||
Authors | Fleming, J.R. / Morgan, R.E. / Fyfe, P.K. / Kelly, S.M. / Hunter, W.N. | ||||||
Citation | Journal: FEBS J. / Year: 2013 Title: The Architecture of Trypanosoma Brucei Tubulin-Binding Cofactor B and Implications for Function. Authors: Fleming, J.R. / Morgan, R.E. / Fyfe, P.K. / Kelly, S.M. / Hunter, W.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4b6w.cif.gz | 46.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4b6w.ent.gz | 36.8 KB | Display | PDB format |
PDBx/mmJSON format | 4b6w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b6/4b6w ftp://data.pdbj.org/pub/pdb/validation_reports/b6/4b6w | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 10080.010 Da / Num. of mol.: 1 / Fragment: TBC-B UBL DOMAIN, RESIDUES 2-87 Source method: isolated from a genetically manipulated source Details: DOMAIN OBTAINED VIA CHYMOTRYPSIN PROTEOLYIS OF FULL LENGTH TBC-B PROTEIN Source: (gene. exp.) TRYPANOSOMA BRUCEI BRUCEI STRAIN 927/4 GUTAT10.1 (eukaryote) Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA PLYSS / References: UniProt: Q388K4 |
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#2: Chemical | ChemComp-EDO / |
#3: Water | ChemComp-HOH / |
Sequence details | POLYPEPTID |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.98 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→38.6 Å / Num. obs: 4631 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 12.7 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 15.4 |
Reflection shell | Resolution: 2.35→2.48 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 3.3 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 2.35→36.01 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.946 / SU B: 10.8 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R: 0.317 / ESU R Free: 0.213 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.28 Å2
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Refinement step | Cycle: LAST / Resolution: 2.35→36.01 Å
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