+Open data
-Basic information
Entry | Database: PDB / ID: 1l7i | ||||||
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Title | Crystal Structure of the anti-ErbB2 Fab2C4 | ||||||
Components | (chimera of Fab2C4: "humanized" murine monoclonal antibody) x 2 | ||||||
Keywords | IMMUNE SYSTEM / Ig domain / Fab fragment | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Vajdos, F.F. / Adams, C.W. / Breece, T.N. / Presta, L.G. / de Vos, A.M. / Sidhu, S.S. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2002 Title: Comprehensive functional maps of the antigen-binding site of an anti-ErbB2 antibody obtained with shotgun scanning mutagenesis. Authors: Vajdos, F.F. / Adams, C.W. / Breece, T.N. / Presta, L.G. / de Vos, A.M. / Sidhu, S.S. | ||||||
History |
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Remark 999 | sequence an appropriate sequence database reference was not available at the time of processing. ...sequence an appropriate sequence database reference was not available at the time of processing. Fab2C4 is a "humanized" murine monoclonal antibody, with the following residues corresponding to the human Ig sequence: L1-L23, L35-L49, L57-L88, L98-L214, H1-H25, H36-H49, H66-H68, H70, H72, H74-H94, H102-223. RESIDUES L24-L34, L50-L56, L89-L97, H26-H35, H50-H65, H69, H71, H73, H95-H102 CORRESPOND TO THE ORIGINAL MURINE SEQUENCE. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1l7i.cif.gz | 101.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1l7i.ent.gz | 80.3 KB | Display | PDB format |
PDBx/mmJSON format | 1l7i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1l7i_validation.pdf.gz | 448.2 KB | Display | wwPDB validaton report |
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Full document | 1l7i_full_validation.pdf.gz | 455.8 KB | Display | |
Data in XML | 1l7i_validation.xml.gz | 22.4 KB | Display | |
Data in CIF | 1l7i_validation.cif.gz | 32.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l7/1l7i ftp://data.pdbj.org/pub/pdb/validation_reports/l7/1l7i | 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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Unit cell |
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Details | The biological assembly is a heterodimer of heavy and light chains. |
-Components
#1: Antibody | Mass: 23548.152 Da / Num. of mol.: 1 / Fragment: light chain (residues 1-214) Source method: isolated from a genetically manipulated source Details: The chimera consists of the human Ig and the original murine sequence Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q7Z3Y4 | ||
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#2: Antibody | Mass: 23674.486 Da / Num. of mol.: 1 / Fragment: heavy chain (residues 1-216) Source method: isolated from a genetically manipulated source Details: The chimera consists of the human Ig and the original murine sequence Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q7Z5W1 | ||
#3: Chemical | #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: 2.19 Å3/Da / Density % sol: 43.71 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 35%-45% saturated (NH4)2SO4, 0.1 M Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K | ||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting drop / Details: used microseeding | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 30, 2000 |
Radiation | Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→15 Å / Num. all: 36884 / Num. obs: 36884 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Biso Wilson estimate: 14.9 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 5.2 |
Reflection shell | Resolution: 1.8→1.9 Å / Rmerge(I) obs: 0.328 / Mean I/σ(I) obs: 1.4 / % possible all: 97.6 |
Reflection | *PLUS Lowest resolution: 15 Å / Num. measured all: 85734 |
Reflection shell | *PLUS % possible obs: 97.6 % / Redundancy: 2.3 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→14.39 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1429863.38 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 24 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→14.39 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS % reflection Rfree: 5 % / Rfactor Rfree: 0.23 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rwork: 0.27 |