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- PDB-5i76: Crystal structure of FM318, a recombinant Fab adopted from cetuximab -

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Basic information

Entry
Database: PDB / ID: 5i76
TitleCrystal structure of FM318, a recombinant Fab adopted from cetuximab
Components
  • FM318_heavy_cahin
  • FM318_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: 1.922 Å
AuthorsSim, D.W. / Kim, J.H. / Seok, S.H. / Seo, M.D. / Kim, Y.P. / Won, H.S.
CitationJournal: Appl.Microbiol.Biotechnol. / Year: 2016
Title: Bacterial production and structure-functional validation of a recombinant antigen-binding fragment (Fab) of an anti-cancer therapeutic antibody targeting epidermal growth factor receptor.
Authors: Kim, J.H. / Sim, D.W. / Park, D. / Jung, T.G. / Lee, S. / Oh, T. / Ha, J.R. / Seok, S.H. / Seo, M.D. / Kang, H.C. / Kim, Y.P. / Won, H.S.
History
DepositionFeb 16, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Data collection / Database references / Category: citation / diffrn_detector / Item: _citation.journal_id_CSD / _diffrn_detector.detector
Revision 1.2Nov 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 1.3Oct 30, 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: FM318_light_chain
B: FM318_heavy_cahin
C: FM318_light_chain
D: FM318_heavy_cahin


Theoretical massNumber of molelcules
Total (without water)95,1864
Polymers95,1864
Non-polymers00
Water17,276959
1
A: FM318_light_chain
B: FM318_heavy_cahin


Theoretical massNumber of molelcules
Total (without water)47,5932
Polymers47,5932
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint-19 kcal/mol
Surface area19260 Å2
MethodPISA
2
C: FM318_light_chain
D: FM318_heavy_cahin


Theoretical massNumber of molelcules
Total (without water)47,5932
Polymers47,5932
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-22 kcal/mol
Surface area19280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.482, 68.037, 97.689
Angle α, β, γ (deg.)90.00, 101.85, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody FM318_light_chain


Mass: 23519.963 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens/Mus musculus xenograft (mammal)
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
#2: Antibody FM318_heavy_cahin


Mass: 24072.916 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens/Mus musculus xenograft (mammal)
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 959 / 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: 2.48 Å3/Da / Density % sol: 50.34 %
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: 7A (6B, 6C1) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Sep 30, 2014
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: 1.92→27.72 Å / Num. obs: 69631 / % possible obs: 98.4 % / Redundancy: 7.5 % / Biso Wilson estimate: 21.03 Å2 / Rsym value: 0.076 / Net I/σ(I): 45.25
Reflection shellResolution: 1.93→1.96 Å / Redundancy: 7.6 % / Mean I/σ(I) obs: 11.26 / % possible all: 97.4

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Processing

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

1yy8


Resolution: 1.922→27.717 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.16
RfactorNum. reflection% reflection
Rfree0.201 3514 5.05 %
Rwork0.1659 --
obs0.1677 69631 98.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.922→27.717 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6587 0 0 959 7546
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0126750
X-RAY DIFFRACTIONf_angle_d1.1359200
X-RAY DIFFRACTIONf_dihedral_angle_d10.6594021
X-RAY DIFFRACTIONf_chiral_restr0.0641039
X-RAY DIFFRACTIONf_plane_restr0.0071178
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9219-1.94830.23311250.1832394X-RAY DIFFRACTION88
1.9483-1.97610.22951490.17932548X-RAY DIFFRACTION97
1.9761-2.00560.2241440.16932640X-RAY DIFFRACTION98
2.0056-2.03690.24191140.17292624X-RAY DIFFRACTION98
2.0369-2.07030.24581370.16592685X-RAY DIFFRACTION98
2.0703-2.1060.20461600.17142551X-RAY DIFFRACTION98
2.106-2.14420.23051240.1692640X-RAY DIFFRACTION98
2.1442-2.18550.22881360.16612629X-RAY DIFFRACTION98
2.1855-2.23010.21841550.17562631X-RAY DIFFRACTION98
2.2301-2.27850.23961500.16882632X-RAY DIFFRACTION98
2.2785-2.33150.21471340.16432664X-RAY DIFFRACTION98
2.3315-2.38980.2221380.16962626X-RAY DIFFRACTION98
2.3898-2.45440.22041330.17232642X-RAY DIFFRACTION99
2.4544-2.52650.20491270.17382687X-RAY DIFFRACTION99
2.5265-2.6080.20881390.17422663X-RAY DIFFRACTION99
2.608-2.70120.241220.17682665X-RAY DIFFRACTION99
2.7012-2.80920.18931310.16742678X-RAY DIFFRACTION99
2.8092-2.93690.21991300.17312672X-RAY DIFFRACTION99
2.9369-3.09160.19271570.16962653X-RAY DIFFRACTION99
3.0916-3.2850.21041560.16212675X-RAY DIFFRACTION99
3.285-3.53820.18531470.1612661X-RAY DIFFRACTION99
3.5382-3.89340.16431490.15072706X-RAY DIFFRACTION99
3.8934-4.45470.18441580.1422690X-RAY DIFFRACTION100
4.4547-5.60490.15081460.14262726X-RAY DIFFRACTION99
5.6049-27.71950.22221530.21052735X-RAY DIFFRACTION98

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