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Yorodumi- PDB-2bmk: Fab fragment of PLP-dependent catalytic antibody 15A9 in complex ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2bmk | ||||||
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Title | Fab fragment of PLP-dependent catalytic antibody 15A9 in complex with phosphopyridoxyl-D-alanine | ||||||
Components |
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Keywords | 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 Function and homology information | ||||||
Biological species | MUS MUSCULUS (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Golinelli-Pimpaneau, B. / Christen, P. | ||||||
Citation | Journal: J. Biol. Chem. / Year: 2006 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 |
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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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2bmk.cif.gz | 182.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bmk.ent.gz | 144.7 KB | Display | PDB format |
PDBx/mmJSON format | 2bmk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bm/2bmk ftp://data.pdbj.org/pub/pdb/validation_reports/bm/2bmk | HTTPS FTP |
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-Related structure data
Related structure data | 1wcbSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Antibody | Mass: 23355.787 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse) / Cell line (production host): 15A9 MURINE HYBRIDOMA / Production host: MUS MUSCULUS (house mouse) / Strain (production host): BALB/C #2: Antibody | Mass: 24501.449 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse) / Cell line (production host): 15A9 MURINE HYBRIDOMA / Production host: MUS MUSCULUS (house mouse) / Strain (production host): BALB/C #3: Chemical | ChemComp-IOD / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.8 Å3/Da / Density % sol: 32.2 % |
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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 |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 |
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 |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1WCB Resolution: 2.3→40 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Bsol: 37.74 Å2 / ksol: 0.328199 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.7 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.4 Å / Total num. of bins used: 8 /
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Xplor file |
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