[English] 日本語
![](img/lk-miru.gif)
- PDB-2pmv: Crystal Structure of Human Intrinsic Factor- Cobalamin Complex at... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2pmv | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal Structure of Human Intrinsic Factor- Cobalamin Complex at 2.6 A Resolution | |||||||||
![]() | Gastric intrinsic factor | |||||||||
![]() | TRANSPORT PROTEIN / Cobalamin transport protein Alpha6-Alpha6 motif two domain protein | |||||||||
Function / homology | ![]() Defective CBLIF causes IFD / Defective AMN causes MGA1 / Defective CUBN causes MGA1 / cargo receptor ligand activity / Uptake of dietary cobalamins into enterocytes / cobalt ion transport / cobalamin transport / cobalamin binding / microvillus / lysosomal lumen ...Defective CBLIF causes IFD / Defective AMN causes MGA1 / Defective CUBN causes MGA1 / cargo receptor ligand activity / Uptake of dietary cobalamins into enterocytes / cobalt ion transport / cobalamin transport / cobalamin binding / microvillus / lysosomal lumen / endosome / apical plasma membrane / extracellular space / extracellular region Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Mathews, F.S. / Gordon, M.M. / Chen, Z. / Rajashankar, K.R. / Ealick, S.E. / Alpers, D.H. / Sukumar, N. | |||||||||
![]() | ![]() Title: Crystal structure of human intrinsic factor: Cobalamin complex at 2.6-A resolution Authors: Mathews, F.S. / Gordon, M.M. / Chen, Z. / Rajashankar, K.R. / Ealick, S.E. / Alpers, D.H. / Sukumar, N. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 263.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 216.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 2 MB | Display | |
Data in XML | ![]() | 62.6 KB | Display | |
Data in CIF | ![]() | 84.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
3 | ![]()
| ||||||||
4 | ![]()
| ||||||||
Unit cell |
| ||||||||
Details | The biological assembly is a monomer. |
-
Components
#1: Protein | Mass: 43448.379 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 51.9 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 10% PEG20000, 100mM MES, 20mM CaCL2 and 9mM BaCL2, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.6059 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. all: 61149 / Num. obs: 55707 / % possible obs: 91.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 36.5 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 16.5 |
Reflection shell | Resolution: 2.5→2.6 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.491 / Mean I/σ(I) obs: 2.2 / % possible all: 54.7 |
-
Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| |||||||||||||||||||||||||
Displacement parameters | Biso mean: 56 Å2 | |||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→37.53 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 2.6→2.76 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
|