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- PDB-7om5: Anti-EGFR nanobody EgB4 -

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Basic information

Entry
Database: PDB / ID: 7om5
TitleAnti-EGFR nanobody EgB4
ComponentsNanobody EgB4
KeywordsIMMUNE SYSTEM / EGFR / nanobody / cancer / signaling
Biological speciesLama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsZeronian, M.R. / Janssen, B.J.C.
CitationJournal: Bmc Mol Cell Biol / Year: 2022
Title: Structural insights into the non-inhibitory mechanism of the anti-EGFR EgB4 nanobody.
Authors: Zeronian, M.R. / Doulkeridou, S. / van Bergen En Henegouwen, P.M.P. / Janssen, B.J.C.
History
DepositionMay 21, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nanobody EgB4
B: Nanobody EgB4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6145
Polymers28,3912
Non-polymers2233
Water3,171176
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1660 Å2
ΔGint-41 kcal/mol
Surface area12300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.539, 71.576, 53.204
Angle α, β, γ (deg.)90.000, 91.480, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody Nanobody EgB4


Mass: 14195.455 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.59 Å3/Da / Density % sol: 52.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.05 M zinc acetate and 20 % w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9688 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9688 Å / Relative weight: 1
ReflectionResolution: 1.48→42.69 Å / Num. obs: 47214 / % possible obs: 98 % / Redundancy: 3.4 % / CC1/2: 0.99 / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.078 / Rrim(I) all: 0.147 / Net I/σ(I): 5.4
Reflection shellResolution: 1.48→1.5 Å / Redundancy: 3.4 % / Rmerge(I) obs: 1.681 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 2189 / CC1/2: 0.277 / Rpim(I) all: 1.037 / Rrim(I) all: 1.981 / % possible all: 93

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
PHASERphasing
Aimlessdata scaling
DIALSdata reduction
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KRN

4krn


Resolution: 1.48→42.69 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.958 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.067 / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2051 2262 4.8 %RANDOM
Rwork0.1773 ---
obs0.1786 44926 97.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 67.05 Å2 / Biso mean: 16.232 Å2 / Biso min: 7.79 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å2-0 Å2-0.9 Å2
2---0.66 Å2-0 Å2
3---0.44 Å2
Refinement stepCycle: final / Resolution: 1.48→42.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1959 0 8 176 2143
Biso mean--15.69 26.47 -
Num. residues----255
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0132108
X-RAY DIFFRACTIONr_bond_other_d0.0370.0181792
X-RAY DIFFRACTIONr_angle_refined_deg1.6831.6392881
X-RAY DIFFRACTIONr_angle_other_deg2.5051.584175
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8425285
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.67421.441118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.21615325
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1021517
X-RAY DIFFRACTIONr_chiral_restr0.0780.2270
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022481
X-RAY DIFFRACTIONr_gen_planes_other0.0180.02506
LS refinement shellResolution: 1.48→1.517 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.296 160 -
Rwork0.29 3129 -
obs--94.24 %

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