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- PDB-5icy: Cetuximab Fab in complex with linear meditope -

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Basic information

Entry
Database: PDB / ID: 5icy
TitleCetuximab Fab in complex with linear meditope
Components
  • Cetuximab Fab heavy chain
  • Cetuximab Fab light chain
  • Meditope
KeywordsIMMUNE SYSTEM / antibody / anti-EGFR
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / PHOSPHATE ION
Function and homology information
Biological speciesMUS MUSCULUS (house mouse)
HOMO SAPIENS (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsBzymek, K.P. / Williams, J.C.
CitationJournal: 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
DepositionFeb 23, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2017Group: Database references / Derived calculations / Category: citation / pdbx_struct_oper_list
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _pdbx_struct_oper_list.symmetry_operation
Revision 2.0Dec 25, 2019Group: Derived calculations / Polymer sequence / Category: entity_poly / pdbx_struct_mod_residue
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id
Revision 2.1Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cetuximab Fab light chain
B: Cetuximab Fab heavy chain
C: Cetuximab Fab light chain
D: Cetuximab Fab heavy chain
E: Meditope
F: Meditope
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,53813
Polymers96,8746
Non-polymers6657
Water9,152508
1
A: Cetuximab Fab light chain
B: Cetuximab Fab heavy chain
E: Meditope
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8177
Polymers48,4373
Non-polymers3804
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5960 Å2
ΔGint-57 kcal/mol
Surface area18620 Å2
MethodPISA
2
C: Cetuximab Fab light chain
D: Cetuximab Fab heavy chain
F: Meditope
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7226
Polymers48,4373
Non-polymers2853
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5670 Å2
ΔGint-44 kcal/mol
Surface area18460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.180, 82.890, 212.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody Cetuximab Fab light chain


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 Cetuximab Fab heavy chain


Mass: 23708.475 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS, HOMO SAPIENS / Production host: unidentified (others)
#3: Protein/peptide Meditope


Mass: 1440.626 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 508 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.92 Å3/Da / Density % sol: 57.92 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 10, 2012
RadiationMonochromator: VARIMAX / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→34.82 Å / Num. obs: 40040 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 4.68 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 20.15
Reflection shellResolution: 2.5→2.57 Å / Redundancy: 3.53 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 5.87 / % possible all: 96.1

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PHENIX1.8_1069refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4gw1

4gw1


Resolution: 2.5→34.82 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 2.02 / Phase error: 19.29
RfactorNum. reflection% reflection
Rfree0.206 2002 5 %
Rwork0.16 --
obs0.162 40037 99.6 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 1 Å
Refinement stepCycle: LAST / Resolution: 2.5→34.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6722 0 35 508 7265
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086971
X-RAY DIFFRACTIONf_angle_d1.1129497
X-RAY DIFFRACTIONf_dihedral_angle_d13.2372490
X-RAY DIFFRACTIONf_chiral_restr0.0731070
X-RAY DIFFRACTIONf_plane_restr0.0041215
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.56260.2971350.21062568X-RAY DIFFRACTION96
2.5626-2.63180.27941390.18192643X-RAY DIFFRACTION100
2.6318-2.70930.25441420.18072701X-RAY DIFFRACTION100
2.7093-2.79670.25151420.17582692X-RAY DIFFRACTION100
2.7967-2.89660.23781410.16662689X-RAY DIFFRACTION100
2.8966-3.01250.20991420.16612697X-RAY DIFFRACTION100
3.0125-3.14950.20321420.16082689X-RAY DIFFRACTION100
3.1495-3.31540.21851430.15422729X-RAY DIFFRACTION100
3.3154-3.5230.18951420.15462683X-RAY DIFFRACTION100
3.523-3.79470.18981440.15212744X-RAY DIFFRACTION100
3.7947-4.1760.18181430.13982726X-RAY DIFFRACTION100
4.176-4.77890.16121450.12372757X-RAY DIFFRACTION100
4.7789-6.01590.18141470.15072785X-RAY DIFFRACTION100
6.0159-34.81990.21451550.20072932X-RAY DIFFRACTION100

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