+
Open data
-
Basic information
Entry | Database: PDB / ID: 1wcb | ||||||
---|---|---|---|---|---|---|---|
Title | PLP-DEPENDENT CATALYTIC ANTIBODY 15A9 IN COMPLEX WITH ITS HAPTEN | ||||||
![]() |
| ||||||
![]() | IMMUNE SYSTEM / CATALYTIC ANTIBODY / TRANSAMINATION / PYRIDOXAL-PHOSPHATE / HAPTEN / PHOSPHOPYRIDOXYL-L-LYSINE | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / IODIDE ION / Chem-PE1![]() | ||||||
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 | ![]() | 189.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 149.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1024 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 42 KB | Display | |
Data in CIF | ![]() | 59.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2bmkC ![]() 1cloS C: citing same article ( S: Starting model for refinement |
---|---|
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 | #4: Chemical | ChemComp-IOD / #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 34.7 % |
---|---|
Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 30% PEG 3350, 200MM SODIUM REMARK 280 IODIDE, 50MM SODIUM ACETATE, PH 6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Feb 24, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→25 Å / Num. obs: 28522 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Biso Wilson estimate: 31.5 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 2.5→2.54 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 5.1 / % possible all: 94.3 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1CLO Resolution: 2.5→40 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0 Stereochemistry target values: MAXIMUM LIKELIHOOD TARGET USING AMPLITUDES Details: THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE ELECTRON DENSITY: ALA H 129, ALA H 130, ARG H 213, ASP H 214, ALA B 129, ALA B 130 THE SIDE-CHAINS OF THE FOLLOWING RESIDUES ARE POORLY DEFINED ...Details: THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE ELECTRON DENSITY: ALA H 129, ALA H 130, ARG H 213, ASP H 214, ALA B 129, ALA B 130 THE SIDE-CHAINS OF THE FOLLOWING RESIDUES ARE POORLY DEFINED BY THE ELECTRON DENSITY AND WERE MODELLED AS ALANINE: SER L 56, LYS L 142, LYS H 43, ARG H 83, GLU H 100C, GLN H 131, SER H 134, SER H 158, GLN H 171, GLU H 191, LYS H 205, LYS H 209, GLN B 131, SER B 134, GLN B 171, LYS B 209
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Bsol: 36.4942 Å2 / ksol: 0.332759 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.6 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→40 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.5→2.52 Å / Total num. of bins used: 50
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|