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- PDB-2v3p: Crystallographic analysis of beta-axial ligand substitutions in c... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2v3p | ||||||
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Title | Crystallographic analysis of beta-axial ligand substitutions in cobalamin bound to transcobalamin | ||||||
![]() | TRANSCOBALAMIN-2 | ||||||
![]() | TRANSPORT PROTEIN / ION TRANSPORT / VITAMIN B12 TRANSPORT PROTEIN / BETA LIGAND SUBSTITUTION | ||||||
Function / homology | ![]() Transport of RCbl within the body / cobalt ion transport / cobalamin transport / cobalamin binding / extracellular space / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wuerges, J. / Geremia, S. / Randaccio, L. | ||||||
![]() | ![]() Title: Vitamin B12 Transport Proteins: Crystallographic Analysis of Beta-Axial Ligand Substitutions in Cobalamin Bound to Transcobalamin. Authors: Wuerges, J. / Geremia, S. / Fedosov, S.N. / Randaccio, L. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. | ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 99.7 KB | Display | ![]() |
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PDB format | ![]() | 74.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1014.3 KB | Display | ![]() |
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Full document | ![]() | 1019.5 KB | Display | |
Data in XML | ![]() | 18.1 KB | Display | |
Data in CIF | ![]() | 25.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2v3nC ![]() 2bbcS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() | ||||
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#2: Chemical | ChemComp-B12 / | ||||
#3: Chemical | #4: Chemical | ChemComp-SO3 / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.1 Å3/Da / Density % sol: 69.9 % / Description: NONE |
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Crystal grow | pH: 8.5 Details: THE PROTEIN AT 0.5 MM IN 1 M NACL, 0.1 M TRIS, PH 7.5 CRYSTALLIZED FROM 28% PEG 8000, 0.2 M MAGNESIUM ACETATE, 0.1 M TRIS PH 8.5, 20% 2-METHYL-2, 4-PENTADIOL, 40 MM (NH4)2SO3. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 30, 2007 |
Radiation | Monochromator: DOUBLE CRYSTAL SI(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→29.3 Å / Num. obs: 16711 / % possible obs: 97.6 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 2.9→3.06 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 1.8 / % possible all: 99.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2BBC Resolution: 2.9→28.98 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.904 / SU B: 25.622 / SU ML: 0.249 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.675 / ESU R Free: 0.342 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. AMINO ACIDS FROM LYS168 TO VAL176 WERE NOT MODELLED DUE TO DISORDER. HIS175 AS UPPER AXIAL LIGAND OF COBALAMIN HAS BEEN DISPLACED BY ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. AMINO ACIDS FROM LYS168 TO VAL176 WERE NOT MODELLED DUE TO DISORDER. HIS175 AS UPPER AXIAL LIGAND OF COBALAMIN HAS BEEN DISPLACED BY EXTERNALLY SUPPLIED SULFITE.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.15 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→28.98 Å
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Refine LS restraints |
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