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Yorodumi- PDB-1wc7: FAB FRAGMENT OF PLP-DEPENDENT CATALYTIC ANTIBODY 15A9 IN COMPLEX ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1wc7 | ||||||
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Title | FAB FRAGMENT OF PLP-DEPENDENT CATALYTIC ANTIBODY 15A9 IN COMPLEX WITH PHOSPHOPYRIDOXYL-L-ALANINE | ||||||
Components |
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Keywords | ANTIBODY / CATALYTIC ANTIBODY / TRANSAMINATION / PYRIDOXAL-PHOSPHATE / PHOSPHOPYRIDOXYL-L-ALANINE | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / IODIDE ION / ALANYL-PYRIDOXAL-5'-PHOSPHATE Function and homology information | ||||||
Biological species | MUS MUSCULUS (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å | ||||||
Authors | Golinelli-Pimpaneau, B. / Christen, P. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2005 Title: Structure of a Pseudomerohedrally Twinned Monoclinic Crystal Form of a Pyridoxal Phosphate-Dependent Catalytic Antibody Authors: Golinelli-Pimpaneau, B. #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 | 1wc7.cif.gz | 177.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1wc7.ent.gz | 139.1 KB | Display | PDB format |
PDBx/mmJSON format | 1wc7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1wc7_validation.pdf.gz | 753.5 KB | Display | wwPDB validaton report |
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Full document | 1wc7_full_validation.pdf.gz | 829.6 KB | Display | |
Data in XML | 1wc7_validation.xml.gz | 41.3 KB | Display | |
Data in CIF | 1wc7_validation.cif.gz | 55.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wc/1wc7 ftp://data.pdbj.org/pub/pdb/validation_reports/wc/1wc7 | HTTPS FTP |
-Related structure data
Related structure data | 15a9S S: Starting model for refinement |
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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 | ChemComp-PP3 / | #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: 1.91 Å3/Da / Density % sol: 35.8 % |
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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 |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 |
Detector | 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: 34338 / % possible obs: 99.8 % / Redundancy: 3.31 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 3.09 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 2 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: FAB 15A9 IN COMPLEX WITH PPL-L-LYSINE Resolution: 2.33→20 Å / Num. parameters: 26448 / Num. restraintsaints: 35417 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
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Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 6611 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.33→20 Å
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Refine LS restraints |
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