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Yorodumi- PDB-2bbc: Structure of Cobalamin-complexed Bovine Transcobalamin in trigona... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2bbc | ||||||
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Title | Structure of Cobalamin-complexed Bovine Transcobalamin in trigonal crystal form | ||||||
Components | Transcobalamin IITranscobalamin | ||||||
Keywords | TRANSPORT PROTEIN / alpha_6 - alpha_6 barrel | ||||||
Function / homology | Function and homology information Transport of RCbl within the body / cobalt ion transport / cobalamin transport / cobalamin binding / extracellular space / metal ion binding Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Wuerges, J. / Garau, G. / Geremia, S. / Fedosov, S.N. / Petersen, T.E. / Randaccio, L. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2006 Title: Structural basis for mammalian vitamin B12 transport by transcobalamin. Authors: Wuerges, J. / Garau, G. / Geremia, S. / Fedosov, S.N. / Petersen, T.E. / Randaccio, L. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED | ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2bbc.cif.gz | 104.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bbc.ent.gz | 78.2 KB | Display | PDB format |
PDBx/mmJSON format | 2bbc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bb/2bbc ftp://data.pdbj.org/pub/pdb/validation_reports/bb/2bbc | HTTPS FTP |
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-Related structure data
Related structure data | 2bb5C 2bb6SC C: citing same article (ref.) S: Starting model for refinement |
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Similar 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: 46315.219 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: TCN2, TC2 / Production host: Pichia pastoris (fungus) / Strain (production host): SMD 1168 / References: UniProt: Q9XSC9 | ||||
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#2: Chemical | #3: Chemical | #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: 3.97 Å3/Da / Density % sol: 69.03 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 28% PEG 8000, 0.2M magnesium acetate, 20% 2-methyl-2,4-pentadiol, 0.1M TRIS 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 1, 2004 |
Radiation | Monochromator: Double Crystal (Si111, Si220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. all: 29190 / Num. obs: 29142 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 55.7 Å2 / Rmerge(I) obs: 0.054 / Χ2: 0.922 / Net I/σ(I): 24.3 |
Reflection shell | Resolution: 2.4→2.49 Å / % possible obs: 98.7 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.607 / Mean I/σ(I) obs: 2.1 / Num. measured obs: 2875 / Num. unique all: 2875 / Χ2: 1.096 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Structure of Bovine Transcobalamin in monoclinic crystal form (PDB 2BB6). Resolution: 2.4→20 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.929 / SU B: 12.981 / SU ML: 0.16 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.251 / ESU R Free: 0.208 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS
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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: 54.845 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.461 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A
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