[English] 日本語
![](img/lk-miru.gif)
- PDB-2bmk: Fab fragment of PLP-dependent catalytic antibody 15A9 in complex ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2bmk | ||||||
---|---|---|---|---|---|---|---|
Title | Fab fragment of PLP-dependent catalytic antibody 15A9 in complex with phosphopyridoxyl-D-alanine | ||||||
![]() |
| ||||||
![]() | IMMUNE SYSTEM / CATALYTIC ANTIBODY / TRANSAMINATION / PYRIDOXAL-PHOSPHATE / HAPTEN / PHOSPHOPYRIDOXYL-L-LYSINE | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / IODIDE ION / N-(5'-PHOSPHOPYRIDOXYL)-D-ALANINE![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Golinelli-Pimpaneau, B. / Christen, P. | ||||||
![]() | ![]() Title: Structural basis for D-amino acid transamination by the pyridoxal 5'-phosphate-dependent catalytic antibody 15A9. Authors: Golinelli-Pimpaneau, B. / Luthi, C. / Christen, P. #1: Journal: J.Biol.Chem. / Year: 1997 Title: Monoclonal Antibodies Against N-Alpha-(5'-Phosphopyridoxyl)-L-Lysine. Authors: Gramatikova, S.I. / Christen, P. | ||||||
History |
| ||||||
Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 182.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 144.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 517.6 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 541 KB | Display | |
Data in XML | ![]() | 21.7 KB | Display | |
Data in CIF | ![]() | 33.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1wcbSC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||||
2 | ![]()
| ||||||||||||
Unit cell |
| ||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
|
-
Components
#1: Antibody | Mass: 23355.787 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Antibody | Mass: 24501.449 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Chemical | ChemComp-IOD / #4: Chemical | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 1.8 Å3/Da / Density % sol: 32.2 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 6 Details: 30%PEG 3350, 200MM SODIUM IODIDE, 50MM SODIUM ACETATE, PH6, VAPOR DIFFUSION, TEMPERATURE 298K, pH 6.00 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 4, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.931 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→40 Å / Num. obs: 32263 / % possible obs: 99.9 % / Redundancy: 3.7 % / Biso Wilson estimate: 44.06 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.2 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2.5 / % possible all: 99.9 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1WCB Resolution: 2.3→40 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Bsol: 37.74 Å2 / ksol: 0.328199 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.7 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→40 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.3→2.4 Å / Total num. of bins used: 8 /
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|