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- PDB-5ivz: Cetuximab Fab in complex with Arg8Cir meditope variant -

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Basic information

Entry
Database: PDB / ID: 5ivz
TitleCetuximab Fab in complex with Arg8Cir meditope variant
Components
  • Cetuximab Fab, heavy chain
  • Cetuximab Fab, light chain
  • Meditope variant
KeywordsIMMUNE SYSTEM
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: 2.48 Å
AuthorsBzymek, K.P. / Williams, J.C.
CitationJournal: 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
DepositionMar 21, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2016Group: Database references
Revision 1.2Dec 13, 2017Group: Database references / Derived calculations / Category: citation / pdbx_struct_oper_list
Item: _citation.journal_abbrev / _citation.page_first ..._citation.journal_abbrev / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Sep 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 ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 2.1Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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 variant
F: Meditope variant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,16710
Polymers96,7886
Non-polymers3804
Water9,674537
1
A: Cetuximab Fab, light chain
B: Cetuximab Fab, heavy chain
E: Meditope variant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5845
Polymers48,3943
Non-polymers1902
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Cetuximab Fab, light chain
D: Cetuximab Fab, heavy chain
F: Meditope variant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5845
Polymers48,3943
Non-polymers1902
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.340, 82.570, 212.050
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 variant


Mass: 1380.551 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.: 4 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 537 / 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: 2.91 Å3/Da / Density % sol: 57.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M citric acid, 0.1 M sodium phosphate dibasic, 0.4 M potassium phosphate dibasic, 1.6 M sodium phosphate monobasic

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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: Aug 17, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.48→34.29 Å / Num. obs: 40202 / % possible obs: 98.2 % / Redundancy: 6.2 % / Net I/σ(I): 38.2
Reflection shellResolution: 2.48→2.54 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 11.4

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155)refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4gw1

4gw1


Resolution: 2.48→34.29 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 21.5
RfactorNum. reflection% reflection
Rfree0.2298 2011 5 %
Rwork0.1761 --
obs0.1788 40196 98.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å
Refinement stepCycle: LAST / Resolution: 2.48→34.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6714 0 20 537 7271
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076951
X-RAY DIFFRACTIONf_angle_d0.9169480
X-RAY DIFFRACTIONf_dihedral_angle_d12.0464138
X-RAY DIFFRACTIONf_chiral_restr0.0541064
X-RAY DIFFRACTIONf_plane_restr0.0051215
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4803-2.54230.30481310.20192475X-RAY DIFFRACTION91
2.5423-2.6110.27751430.19742722X-RAY DIFFRACTION99
2.611-2.68780.27031450.18162763X-RAY DIFFRACTION100
2.6878-2.77460.2441430.18062704X-RAY DIFFRACTION100
2.7746-2.87370.2441430.17962725X-RAY DIFFRACTION100
2.8737-2.98870.2681460.182764X-RAY DIFFRACTION100
2.9887-3.12460.22531430.18692724X-RAY DIFFRACTION100
3.1246-3.28920.23811460.19022767X-RAY DIFFRACTION100
3.2892-3.49510.2231450.1752771X-RAY DIFFRACTION100
3.4951-3.76470.27831300.21562454X-RAY DIFFRACTION88
3.7647-4.14290.22641420.16252695X-RAY DIFFRACTION97
4.1429-4.74110.15291470.13022806X-RAY DIFFRACTION100
4.7411-5.96820.18361500.14412839X-RAY DIFFRACTION100
5.9682-34.29280.22941570.19962976X-RAY DIFFRACTION100

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