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- PDB-5gz0: Crystal structure of FM329, a recombinant Fab adopted from cetuximab -

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Basic information

Entry
Database: PDB / ID: 5gz0
TitleCrystal structure of FM329, a recombinant Fab adopted from cetuximab
Components
  • FM329 heavy chain
  • FM329 light chain
KeywordsIMMUNE SYSTEM / Antibody fragment / Recombinant Fab / Cetuximab / EGFR
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens/Mus musculus xenograft (mammal)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSim, D.W. / Kim, J.H. / Kim, Y.P. / Won, H.S.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
Korea Small and Medium Business AdministrationC0333276 Korea, Republic Of
CitationJournal: To Be Published
Title: Crystal structure of FM329, a recombinant Fab adopted from cetuximab
Authors: Sim, D.W. / Kim, J.H. / Kim, Y.P. / Won, H.S.
History
DepositionSep 26, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 4, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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
Revision 1.2Oct 16, 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: FM329 light chain
B: FM329 heavy chain
C: FM329 light chain
D: FM329 heavy chain


Theoretical massNumber of molelcules
Total (without water)95,0504
Polymers95,0504
Non-polymers00
Water13,007722
1
A: FM329 light chain
B: FM329 heavy chain


Theoretical massNumber of molelcules
Total (without water)47,5252
Polymers47,5252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint-20 kcal/mol
Surface area19300 Å2
MethodPISA
2
C: FM329 light chain
D: FM329 heavy chain


Theoretical massNumber of molelcules
Total (without water)47,5252
Polymers47,5252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint-22 kcal/mol
Surface area19120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.521, 68.031, 97.780
Angle α, β, γ (deg.)90.00, 101.84, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody FM329 light chain


Mass: 23552.973 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens/Mus musculus xenograft (mammal)
Plasmid: pACYCDuet-1 / Details (production host): Protein co-expression / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
#2: Antibody FM329 heavy chain


Mass: 23971.812 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens/Mus musculus xenograft (mammal)
Plasmid: pACYCDuet-1 / Details (production host): Protein co-expression / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 722 / 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: 2.39 Å3/Da / Density % sol: 50.48 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20% (w/v) PEG 3000, 100 mM Imidazole, Hydrochloric acid pH 8.0, 200 mM Zinc acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: AREA DETECTOR / Date: Feb 23, 2016
RadiationMonochromator: DCM Si (111) Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.69→49.11 Å / Num. obs: 101903 / % possible obs: 99.6 % / Redundancy: 4.1 % / Biso Wilson estimate: 20.27 Å2 / Rsym value: 0.083 / Net I/σ(I): 28.08
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 3.14 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
HKL-2000data processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YY8

1yy8


Resolution: 1.7→47.85 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.53
RfactorNum. reflection% reflection
Rfree0.2265 2000 1.96 %
Rwork0.1878 --
obs0.1885 101874 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.7→47.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6612 0 0 722 7334
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016776
X-RAY DIFFRACTIONf_angle_d1.0829232
X-RAY DIFFRACTIONf_dihedral_angle_d11.0054036
X-RAY DIFFRACTIONf_chiral_restr0.0641036
X-RAY DIFFRACTIONf_plane_restr0.0071186
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6999-1.74240.25071380.22276897X-RAY DIFFRACTION96
1.7424-1.78950.2891410.21497050X-RAY DIFFRACTION99
1.7895-1.84220.2591430.20987121X-RAY DIFFRACTION99
1.8422-1.90170.26171420.20147087X-RAY DIFFRACTION99
1.9017-1.96960.23661420.19557107X-RAY DIFFRACTION100
1.9696-2.04850.23661430.18857131X-RAY DIFFRACTION100
2.0485-2.14170.21211430.18657141X-RAY DIFFRACTION100
2.1417-2.25460.20681430.18487150X-RAY DIFFRACTION100
2.2546-2.39590.24591420.18847122X-RAY DIFFRACTION100
2.3959-2.58090.22061450.19797197X-RAY DIFFRACTION100
2.5809-2.84060.24861430.19947178X-RAY DIFFRACTION100
2.8406-3.25150.21811450.19167183X-RAY DIFFRACTION100
3.2515-4.09620.21451440.17537207X-RAY DIFFRACTION100
4.0962-47.86910.21311460.17497303X-RAY DIFFRACTION99

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