+Open data
-Basic information
Entry | Database: PDB / ID: 3eo9 | ||||||
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Title | Crystal structure the Fab fragment of Efalizumab | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Efalizumab / Fab / antibody | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Li, S. / Ding, J. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2009 Title: Efalizumab binding to the LFA-1 alphaL I domain blocks ICAM-1 binding via steric hindrance. Authors: Li, S. / Wang, H. / Peng, B. / Zhang, M. / Zhang, D. / Hou, S. / Guo, Y. / Ding, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3eo9.cif.gz | 188.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3eo9.ent.gz | 150.6 KB | Display | PDB format |
PDBx/mmJSON format | 3eo9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3eo9_validation.pdf.gz | 430.2 KB | Display | wwPDB validaton report |
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Full document | 3eo9_full_validation.pdf.gz | 435.2 KB | Display | |
Data in XML | 3eo9_validation.xml.gz | 24.6 KB | Display | |
Data in CIF | 3eo9_validation.cif.gz | 37.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eo/3eo9 ftp://data.pdbj.org/pub/pdb/validation_reports/eo/3eo9 | HTTPS FTP |
-Related structure data
Related structure data | 3eoaC 3eobC 1b2wS C: citing same article (ref.) 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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Unit cell |
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-Components
#1: Antibody | Mass: 23436.068 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IGG1 |
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#2: Antibody | Mass: 23622.498 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IGG1 |
#3: Water | ChemComp-HOH / |
Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 55.01 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 15mM citric acid, 12% w/v PEG 3350, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 2, 2007 / Details: Confocal |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. all: 48198 / Num. obs: 47282 / % possible obs: 98.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.2 % / Rmerge(I) obs: 0.083 / Rsym value: 0.083 / Net I/σ(I): 6.3 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.373 / Mean I/σ(I) obs: 1.9 / Num. unique all: 4699 / Rsym value: 0.373 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1B2W Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.936 / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / ESU R: 0.213 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.482 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.846 Å / Total num. of bins used: 20 /
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