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- PDB-5icz: Cetuximab Fab in complex with GQFDLSTRRLKG peptide -

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Basic information

Entry
Database: PDB / ID: 5icz
TitleCetuximab Fab in complex with GQFDLSTRRLKG peptide
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: 2.55 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 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)97,26211
Polymers96,7886
Non-polymers4755
Water7,026390
1
A: Cetuximab Fab light chain
B: Cetuximab Fab heavy chain
E: Meditope
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5845
Polymers48,3943
Non-polymers1902
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5370 Å2
ΔGint-41 kcal/mol
Surface area18790 Å2
MethodPISA
2
C: Cetuximab Fab light chain
D: Cetuximab Fab heavy chain
F: Meditope
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6796
Polymers48,3943
Non-polymers2853
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5610 Å2
ΔGint-42 kcal/mol
Surface area18580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.280, 82.640, 212.500
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: 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)
#3: Protein/peptide Meditope


Mass: 1380.574 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


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


Mass: 18.015 Da / Num. of mol.: 390 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 57.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M CITRIC ACID, 0.1 M SODIUM HYDROGEN PHOSPHATE, 0.5 M POTASSIUM HYDROGEN PHOSPHATE, 1.5 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: Mar 10, 2011
RadiationMonochromator: VARIMAX / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.55→29.66 Å / Num. obs: 36567 / % possible obs: 96.7 % / Observed criterion σ(I): 2 / Redundancy: 5.1 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 20.27
Reflection shellResolution: 2.55→2.62 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.372 / Mean I/σ(I) obs: 4.54 / % possible all: 91.5

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PHENIX1.8.1_1168refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GW1

4gw1


Resolution: 2.55→29.66 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 21.52
RfactorNum. reflection% reflection
Rfree0.221 1829 5 %
Rwork0.171 --
obs0.174 36560 96.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.55→29.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6714 0 25 390 7129
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046931
X-RAY DIFFRACTIONf_angle_d0.8039436
X-RAY DIFFRACTIONf_dihedral_angle_d12.0782468
X-RAY DIFFRACTIONf_chiral_restr0.0531061
X-RAY DIFFRACTIONf_plane_restr0.0041211
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.61910.31321320.2312498X-RAY DIFFRACTION92
2.6191-2.69610.28621360.22152599X-RAY DIFFRACTION96
2.6961-2.7830.28931380.21872611X-RAY DIFFRACTION96
2.783-2.88240.26431380.20722614X-RAY DIFFRACTION96
2.8824-2.99770.27881380.20392641X-RAY DIFFRACTION97
2.9977-3.1340.23111390.1982630X-RAY DIFFRACTION97
3.134-3.29910.24721400.18832656X-RAY DIFFRACTION97
3.2991-3.50540.26681400.17142671X-RAY DIFFRACTION97
3.5054-3.77560.1881420.15462701X-RAY DIFFRACTION97
3.7756-4.15460.16241420.14592689X-RAY DIFFRACTION98
4.1546-4.75370.16671440.12082743X-RAY DIFFRACTION98
4.7537-5.98110.16161450.14112757X-RAY DIFFRACTION98
5.9811-29.66310.24411550.19032921X-RAY DIFFRACTION99

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