+Open data
-Basic information
Entry | Database: PDB / ID: 5id1 | ||||||
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Title | Cetuximab Fab in complex with MPT-Cys meditope | ||||||
Components |
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Keywords | IMMUNE SYSTEM / antibody / anti-EGFR | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / 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: 2.49 Å | ||||||
Authors | Bzymek, K.P. / Williams, J.C. | ||||||
Citation | Journal: Acta Crystallogr F Struct Biol Commun / Year: 2016 Title: Cyclization strategies of meditopes: affinity and diffraction studies of meditope-Fab complexes. Authors: Bzymek, K.P. / Ma, Y. / Avery, K.A. / 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 | 5id1.cif.gz | 188.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5id1.ent.gz | 147.8 KB | Display | PDB format |
PDBx/mmJSON format | 5id1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/id/5id1 ftp://data.pdbj.org/pub/pdb/validation_reports/id/5id1 | HTTPS FTP |
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-Related structure data
Related structure data | 5esqC 5hpmC 5hyqC 5icxC 5icyC 5iczC 5id0C 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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1 |
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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: 23725.504 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, 3 molecules EF
#3: Protein/peptide | Mass: 1457.742 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #4: Sugar | ChemComp-NAG / | |
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-Non-polymers , 2 types, 423 molecules
#5: Chemical | ChemComp-PO4 / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.93 Å3/Da / Density % sol: 57.95 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.1 M CITRIC ACID, 0.1 M SODIUM HYDROGEN PHOSPHATE, 0.4 M POTASSIUM HYDROGEN PHOSPHATE, 1.6 M SODIUM DIHYDROGEN PHOSPHATE, PH 5.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K PH range: 5.5 |
-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: Apr 12, 2012 |
Radiation | Monochromator: VARIMAX / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.49→34.43 Å / Num. obs: 40643 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 7.8 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 39.42 |
Reflection shell | Resolution: 2.49→2.55 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.138 / Mean I/σ(I) obs: 11 / % possible all: 92.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4GW1 Resolution: 2.49→34.43 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 20.87
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.49→34.43 Å
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Refine LS restraints |
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LS refinement shell |
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