+Open data
-Basic information
Entry | Database: PDB / ID: 1um6 | ||||||
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Title | catalytic antibody 21h3 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / catalytic antibody ligand transesterification | ||||||
Function / homology | Function and homology information immunoglobulin complex, circulating / immunoglobulin receptor binding / complement activation, classical pathway / antigen binding / antibacterial humoral response / blood microparticle / extracellular exosome / plasma membrane Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Beuscher IV, A.E. / Reuter, J. / Olson, A.J. / Romesberg, F.E. / Schultz, P.G. / Wirsching, P. / Janda, K.D. / Lerner, R.A. / Stevens, R.C. | ||||||
Citation | Journal: To be Published Title: Structural Studies of an Efficient Catalytic Antibody Operating by Ping-Pong and Induced Fit Mechanisms Authors: Beuscher IV, A.E. / Reuter, J. / Olson, A.J. / Romesberg, F.E. / Schultz, P.G. / Wirsching, P. / Janda, K.D. / Lerner, R.A. / Stevens, R.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1um6.cif.gz | 100.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1um6.ent.gz | 76.4 KB | Display | PDB format |
PDBx/mmJSON format | 1um6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/um/1um6 ftp://data.pdbj.org/pub/pdb/validation_reports/um/1um6 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Antibody | Mass: 23896.475 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) |
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#2: Antibody | Mass: 23002.742 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: Q6PYX1*PLUS |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 41.71 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.25 Details: PEG4000, lithium sulfate, pH 4.25, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 1, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→19.66 Å / Num. all: 37345 / Num. obs: 36641 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 14.2 Å2 / Limit h max: 25 / Limit h min: 0 / Limit k max: 33 / Limit k min: 0 / Limit l max: 76 / Limit l min: 0 / Observed criterion F max: 635244.25 / Observed criterion F min: 0.55 |
Reflection shell | Resolution: 1.8→1.86 Å / % possible all: 96 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→19.66 Å / Rfactor Rfree error: 0.009 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 2
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Solvent computation | Solvent model: CNS bulk solvent model used / Bsol: 35.5494 Å2 / ksol: 0.371044 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 93.52 Å2 / Biso mean: 23.81 Å2 / Biso min: 7.46 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→19.66 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8
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Xplor file |
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