+Open data
-Basic information
Entry | Database: PDB / ID: 2gcy | ||||||
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Title | humanized antibody C25 Fab fragment | ||||||
Components |
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Keywords | IMMUNE SYSTEM / antibody fragment mouse humanized | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å | ||||||
Authors | LaPorte, S.L. / Finer-Moore, J. / Marks, J.D. / Forsyth, C.M. | ||||||
Citation | Journal: To be Published Title: Humanization and structure of antibody clone C25 Authors: LaPorte, S.L. / Finer-Moore, J. / Marks, J.D. / Forsyth, C.M. | ||||||
History |
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Remark 999 | SEQUENCE THERE IS NO SUITABLE SEQUENCE DATABASE REFERENCE AT THE TIME OF PROCESSING. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2gcy.cif.gz | 93.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2gcy.ent.gz | 75.9 KB | Display | PDB format |
PDBx/mmJSON format | 2gcy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2gcy_validation.pdf.gz | 446 KB | Display | wwPDB validaton report |
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Full document | 2gcy_full_validation.pdf.gz | 457.5 KB | Display | |
Data in XML | 2gcy_validation.xml.gz | 19.5 KB | Display | |
Data in CIF | 2gcy_validation.cif.gz | 26.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gc/2gcy ftp://data.pdbj.org/pub/pdb/validation_reports/gc/2gcy | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Antibody | Mass: 23666.188 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: humanized mouse gene / Production host: Cricetulus griseus (Chinese hamster) | ||
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#2: Antibody | Mass: 23488.143 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: humanized mouse gene / Production host: Cricetulus griseus (Chinese hamster) | ||
#3: Chemical | ChemComp-SO4 / #4: 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: 2.71 Å3/Da / Density % sol: 54.58 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: PEG MME 550, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 30, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.11587 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→44.6 Å / Num. all: 17714 / Num. obs: 17714 / % possible obs: 93.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 50.1 Å2 |
-Processing
Software | Name: CNS / Version: 1.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: SAD / Resolution: 2.5→44.6 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 183455.84 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 47.4683 Å2 / ksol: 0.38839 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→44.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.59 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 10
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Xplor file |
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