+Open data
-Basic information
Entry | Database: PDB / ID: 1ngy | ||||||
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Title | Chimeric Mature Fab 7g12-Apo | ||||||
Components |
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Keywords | IMMUNE SYSTEM / antibody / immunoglobulin / antigen binding fragment (Fab) | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Yin, J. / Andryski, S.A. / Beuscher, A.B. / Stevens, R.C. / Schultz, P.G. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2003 Title: Structural evidence for substrate strain in antibody catalysis Authors: Yin, J. / Andryski, S.A. / Beuscher, A.B. / Stevens, R.C. / Schultz, P.G. | ||||||
History |
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Remark 999 | SEQUENCE The gene sequences are derived from a mouse hybridoma. The sequences of the protein chains ...SEQUENCE The gene sequences are derived from a mouse hybridoma. The sequences of the protein chains are not found in any sequence database. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ngy.cif.gz | 92.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ngy.ent.gz | 75.1 KB | Display | PDB format |
PDBx/mmJSON format | 1ngy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ng/1ngy ftp://data.pdbj.org/pub/pdb/validation_reports/ng/1ngy | 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: 23374.963 Da / Num. of mol.: 1 / Fragment: Fab fragment Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus, Homo sapiens / Genus: Mus, Homo / Species: , / Strain: , / Production host: Escherichia coli (E. coli) |
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#2: Antibody | Mass: 23113.029 Da / Num. of mol.: 1 / Fragment: Fab fragment Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus, Homo sapiens / Genus: Mus, Homo / Species: , / Strain: , / Production host: Escherichia coli (E. coli) |
#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: 2.35 Å3/Da / Density % sol: 47.22 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG 2000MME, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 25 ℃ / pH: 6.6 | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-D / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→29.83 Å / Num. all: 22829 / Num. obs: 22829 / Observed criterion σ(F): 0 / Biso Wilson estimate: 26.6 Å2 / Limit h max: 26 / Limit h min: 0 / Limit k max: 43 / Limit k min: 0 / Limit l max: 70 / Limit l min: 0 / Observed criterion F max: 743027.98 / Observed criterion F min: 1.58 |
Reflection | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 20 Å / Num. obs: 22861 / % possible obs: 98.3 % / Num. measured all: 200436 / Rmerge(I) obs: 0.064 |
Reflection shell | *PLUS % possible obs: 97.2 % / Rmerge(I) obs: 0.209 / Mean I/σ(I) obs: 10.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→19.82 Å / Rfactor Rfree error: 0.008 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT
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Solvent computation | Solvent model: CNS bulk solvent model used / Bsol: 45.0965 Å2 / ksol: 0.363159 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 98.71 Å2 / Biso mean: 34.94 Å2 / Biso min: 7.08 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→19.82 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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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 20 Å / % reflection Rfree: 10 % / Rfactor Rwork: 0.236 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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