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- PDB-2xkn: Crystal structure of the Fab fragment of the anti-EGFR antibody 7A7 -

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Basic information

Entry
Database: PDB / ID: 2xkn
TitleCrystal structure of the Fab fragment of the anti-EGFR antibody 7A7
Components(ANTI-EGFR ANTIBODY 7A7) x 2
KeywordsIMMUNE SYSTEM / IMMUNOGLOBULIN
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsTalavera, A. / Mackenzie, J. / Friemann, R. / Krengel, U.
CitationJournal: Mol.Immunol. / Year: 2011
Title: Structure of the Fab Fragment of the Anti-Murine Egfr Antibody 7A7 and Exploration of its Receptor Binding Site.
Authors: Talavera, A. / Mackenzie, J. / Garrido, G. / Friemann, R. / Lopez-Requena, A. / Moreno, E. / Krengel, U.
History
DepositionJul 9, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 15, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2011Group: Database references / Refinement description ...Database references / Refinement description / Source and taxonomy / Version format compliance
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 6, 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: ANTI-EGFR ANTIBODY 7A7
B: ANTI-EGFR ANTIBODY 7A7
C: ANTI-EGFR ANTIBODY 7A7
D: ANTI-EGFR ANTIBODY 7A7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,9228
Polymers95,5044
Non-polymers1,4184
Water20,0331112
1
C: ANTI-EGFR ANTIBODY 7A7
D: ANTI-EGFR ANTIBODY 7A7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1073
Polymers47,7522
Non-polymers3541
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3240 Å2
ΔGint-19.1 kcal/mol
Surface area20020 Å2
MethodPISA
2
A: ANTI-EGFR ANTIBODY 7A7
B: ANTI-EGFR ANTIBODY 7A7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8155
Polymers47,7522
Non-polymers1,0633
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-14.7 kcal/mol
Surface area19200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.034, 57.327, 121.023
Angle α, β, γ (deg.)90.00, 122.51, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2022-

HOH

21A-2136-

HOH

31C-2041-

HOH

41C-2118-

HOH

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Components

#1: Antibody ANTI-EGFR ANTIBODY 7A7


Mass: 24628.053 Da / Num. of mol.: 2 / Fragment: FAB FRAGMENT LIGHT CHAIN (IGG1), RESIDUES 1-223 / Source method: isolated from a natural source / Details: HYBRIDOMA / Source: (natural) MUS MUSCULUS (house mouse)
#2: Antibody ANTI-EGFR ANTIBODY 7A7


Mass: 23124.041 Da / Num. of mol.: 2 / Fragment: FAB FRAGMENT HEAVY CHAIN (IGG1), RESIDUES 1-216 / Source method: isolated from a natural source / Details: HYBRIDOMA / Source: (natural) MUS MUSCULUS (house mouse)
#3: Chemical
ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000


Mass: 354.436 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1112 / 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: 2.5 Å3/Da / Density % sol: 50 % / Description: NONE
Crystal growDetails: 15% PEG 8000, 100 MM TRISAC BUFFER PH 9.0, 10 MM EDTA FROM THE HAMPTON ADDITIVE SCREEN

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931
DetectorDetector: CCD / Date: May 16, 2007 / Details: MIRRORS
RadiationMonochromator: DIAMOND (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 1.4→23 Å / Num. obs: 191075 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Biso Wilson estimate: 14.77 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.1
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 3.1 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HIL

1hil


Resolution: 1.4→22.614 Å / SU ML: 0.19 / σ(F): 1.12 / Phase error: 15.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1765 18824 5 %
Rwork0.1438 --
obs0.1454 374113 99.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.638 Å2 / ksol: 0.376 e/Å3
Displacement parametersBiso mean: 20 Å2
Baniso -1Baniso -2Baniso -3
1-3.6487 Å20 Å2-0.7135 Å2
2---10.022 Å20 Å2
3---6.3733 Å2
Refinement stepCycle: LAST / Resolution: 1.4→22.614 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6466 0 37 1112 7615
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087118
X-RAY DIFFRACTIONf_angle_d1.2479730
X-RAY DIFFRACTIONf_dihedral_angle_d16.2542511
X-RAY DIFFRACTIONf_chiral_restr0.0831091
X-RAY DIFFRACTIONf_plane_restr0.0051255
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.41590.25076240.203611548X-RAY DIFFRACTION98
1.4159-1.43260.23615960.199211809X-RAY DIFFRACTION98
1.4326-1.450.23226150.188811682X-RAY DIFFRACTION98
1.45-1.46840.20075760.177711782X-RAY DIFFRACTION98
1.4684-1.48770.19316410.158911739X-RAY DIFFRACTION98
1.4877-1.50810.18136800.152811742X-RAY DIFFRACTION99
1.5081-1.52960.2085610.154411749X-RAY DIFFRACTION99
1.5296-1.55240.17966580.136111798X-RAY DIFFRACTION99
1.5524-1.57670.16986250.129311662X-RAY DIFFRACTION99
1.5767-1.60250.16086120.120211862X-RAY DIFFRACTION99
1.6025-1.63020.15936620.115511852X-RAY DIFFRACTION99
1.6302-1.65980.16325810.119411808X-RAY DIFFRACTION99
1.6598-1.69170.17946550.116111835X-RAY DIFFRACTION99
1.6917-1.72620.14975940.107111890X-RAY DIFFRACTION99
1.7262-1.76380.14596560.10111781X-RAY DIFFRACTION99
1.7638-1.80480.1586400.106911912X-RAY DIFFRACTION99
1.8048-1.84990.15266000.105511931X-RAY DIFFRACTION99
1.8499-1.89990.16036510.109111833X-RAY DIFFRACTION100
1.8999-1.95570.15466190.11511926X-RAY DIFFRACTION100
1.9557-2.01880.15526650.11311851X-RAY DIFFRACTION100
2.0188-2.09090.15546250.118311941X-RAY DIFFRACTION100
2.0909-2.17460.15845920.119511974X-RAY DIFFRACTION100
2.1746-2.27350.16166050.128611959X-RAY DIFFRACTION100
2.2735-2.39320.18286500.135511941X-RAY DIFFRACTION100
2.3932-2.5430.17476410.136711913X-RAY DIFFRACTION100
2.543-2.7390.17526200.145611931X-RAY DIFFRACTION100
2.739-3.01410.18446510.160711921X-RAY DIFFRACTION100
3.0141-3.44890.18366390.156411903X-RAY DIFFRACTION100
3.4489-4.34020.15186550.139411939X-RAY DIFFRACTION100
4.3402-22.61730.17486350.154311875X-RAY DIFFRACTION99

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