+Open data
-Basic information
Entry | Database: PDB / ID: 5euk | ||||||
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Title | Cetuximab Fab in complex with F3H meditope variant | ||||||
Components |
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Keywords | IMMUNE SYSTEM / antibody / anti-EGFR | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / MESO-ERYTHRITOL / PHOSPHATE ION Function and homology information | ||||||
Biological species | MUS MUSCULUS (house mouse) HOMO SAPIENS (human) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Bzymek, K.P. / Williams, J.C. | ||||||
Citation | Journal: Acta Crystallogr F Struct Biol Commun / Year: 2016 Title: Natural and non-natural amino-acid side-chain substitutions: affinity and diffraction studies of meditope-Fab complexes. Authors: Bzymek, K.P. / Avery, K.A. / Ma, Y. / Horne, D.A. / Williams, J.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5euk.cif.gz | 190.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5euk.ent.gz | 150.1 KB | Display | PDB format |
PDBx/mmJSON format | 5euk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eu/5euk ftp://data.pdbj.org/pub/pdb/validation_reports/eu/5euk | HTTPS FTP |
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-Related structure data
Related structure data | 5etuC 5f88C 5ff6C 5i2iC 5iopC 5ir1C 5itfC 5iv2C 5ivzC 5t1kC 5t1lC 5t1mC 5th2C 4gw1S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
-Antibody , 2 types, 4 molecules ACBD
#1: Antibody | Mass: 23287.705 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS, HOMO SAPIENS / Production host: unidentified (others) #2: Antibody | Mass: 23638.426 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS, HOMO SAPIENS / Production host: unidentified (others) |
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-Protein/peptide / Sugars , 2 types, 4 molecules EF
#3: Protein/peptide | Mass: 1463.729 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #5: Sugar | |
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-Non-polymers , 3 types, 415 molecules
#4: Chemical | ChemComp-PO4 / #6: Chemical | ChemComp-MRY / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.87 Å3/Da / Density % sol: 57.2 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.3 Details: 0.1 M citric acid, 0.1 M sodium phosphate dibasic, 0.4 M potassium phosphate dibasic, 1.6 M sodium phosphate monobasic |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 7, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→32.83 Å / Num. obs: 39428 / % possible obs: 99.2 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.126 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 2.5→2.56 Å / Redundancy: 3 % / Rmerge(I) obs: 0.775 / Mean I/σ(I) obs: 1.8 / % possible all: 92.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4GW1 Resolution: 2.5→32.83 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.27 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→32.83 Å
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Refine LS restraints |
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LS refinement shell |
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