[English] 日本語
Yorodumi- PDB-2v3p: Crystallographic analysis of beta-axial ligand substitutions in c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2v3p | ||||||
---|---|---|---|---|---|---|---|
Title | Crystallographic analysis of beta-axial ligand substitutions in cobalamin bound to transcobalamin | ||||||
Components | TRANSCOBALAMIN-2 | ||||||
Keywords | TRANSPORT PROTEIN / ION TRANSPORT / VITAMIN B12 TRANSPORT PROTEIN / BETA LIGAND SUBSTITUTION | ||||||
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: 2.9 Å | ||||||
Authors | Wuerges, J. / Geremia, S. / Randaccio, L. | ||||||
Citation | Journal: Iubmb Life / Year: 2007 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 |
| ||||||
Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. | ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2v3p.cif.gz | 99.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2v3p.ent.gz | 74.4 KB | Display | PDB format |
PDBx/mmJSON format | 2v3p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2v3p_validation.pdf.gz | 1014.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2v3p_full_validation.pdf.gz | 1019.5 KB | Display | |
Data in XML | 2v3p_validation.xml.gz | 18.1 KB | Display | |
Data in CIF | 2v3p_validation.cif.gz | 25.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v3/2v3p ftp://data.pdbj.org/pub/pdb/validation_reports/v3/2v3p | HTTPS FTP |
-Related structure data
Related structure data | 2v3nC 2bbcS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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) / Organ: BLOOD / Plasmid: PPICZ(ALPHA)-LB / Production host: PICHIA PASTORIS (fungus) / Strain (production host): SMD 1168 / References: UniProt: Q9XSC9 | ||||
---|---|---|---|---|---|
#2: Chemical | ChemComp-B12 / | ||||
#3: Chemical | #4: Chemical | ChemComp-SO3 / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 4.1 Å3/Da / Density % sol: 69.9 % / Description: NONE |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.2 |
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 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→28.98 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|