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- PDB-6df2: Improved anti-phosphotyrosine antibody 4G10-S5-4D5 Fab complexed ... -

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Basic information

Entry
Database: PDB / ID: 6df2
TitleImproved anti-phosphotyrosine antibody 4G10-S5-4D5 Fab complexed with phosphotyrosine peptide
Components
  • Anti-phosphotyrosine antibody c310-4D5 heavy chain
  • Anti-phosphotyrosine antibody c310-4D5 light chain
  • LEU-PTR-LEU
KeywordsIMMUNE SYSTEM / Antibody / RECOMBINATION
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
Model detailsAntibody
AuthorsMou, K. / Leung, K. / Wells, J.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA196276 United States
CitationJournal: J. Am. Chem. Soc. / Year: 2018
Title: Engineering Improved Antiphosphotyrosine Antibodies Based on an Immunoconvergent Binding Motif.
Authors: Mou, Y. / Zhou, X.X. / Leung, K. / Martinko, A.J. / Yu, J.Y. / Chen, W. / Wells, J.A.
History
DepositionMay 13, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 28, 2018Provider: repository / Type: Initial release
Revision 1.1May 1, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 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 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Anti-phosphotyrosine antibody c310-4D5 heavy chain
H: Anti-phosphotyrosine antibody c310-4D5 light chain
D: LEU-PTR-LEU
A: Anti-phosphotyrosine antibody c310-4D5 heavy chain
B: Anti-phosphotyrosine antibody c310-4D5 light chain
C: LEU-PTR-LEU


Theoretical massNumber of molelcules
Total (without water)111,2926
Polymers111,2926
Non-polymers00
Water2,288127
1
L: Anti-phosphotyrosine antibody c310-4D5 heavy chain
H: Anti-phosphotyrosine antibody c310-4D5 light chain
D: LEU-PTR-LEU


Theoretical massNumber of molelcules
Total (without water)55,6463
Polymers55,6463
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3970 Å2
ΔGint-34 kcal/mol
Surface area19000 Å2
MethodPISA
2
A: Anti-phosphotyrosine antibody c310-4D5 heavy chain
B: Anti-phosphotyrosine antibody c310-4D5 light chain
C: LEU-PTR-LEU


Theoretical massNumber of molelcules
Total (without water)55,6463
Polymers55,6463
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3930 Å2
ΔGint-34 kcal/mol
Surface area18360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.510, 110.550, 69.080
Angle α, β, γ (deg.)90.00, 110.38, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody Anti-phosphotyrosine antibody c310-4D5 heavy chain


Mass: 27275.348 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) / Strain (production host): C43(DE3)
#2: Antibody Anti-phosphotyrosine antibody c310-4D5 light chain


Mass: 27883.322 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) / Strain (production host): C43(DE3)
#3: Protein/peptide LEU-PTR-LEU


Mass: 487.484 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H2O

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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: 2.2 Å3/Da / Density % sol: 43.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 26% PEG3350, 0.1M Bis-Tris, and 0.16M ammonium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 8, 2017
RadiationMonochromator: Water-cooled flat double Si(111) Khozu monochromator (DCM)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→84 Å / Num. obs: 29644 / % possible obs: 99.96 % / Redundancy: 13.8 % / Biso Wilson estimate: 45.77 Å2 / Rmerge(I) obs: 0.2101 / Net I/σ(I): 13.2
Reflection shellResolution: 2.6→2.693 Å / Rmerge(I) obs: 1.258 / Num. unique obs: 2940 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
Aimlessdata scaling
PDB_EXTRACT3.24data extraction
MOSFLMdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1bj1

1bj1


Resolution: 2.6→83.656 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2303 1144 3.86 %
Rwork0.1773 --
obs0.1793 29634 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→83.656 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6463 0 0 127 6590
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046626
X-RAY DIFFRACTIONf_angle_d0.7679050
X-RAY DIFFRACTIONf_dihedral_angle_d17.6872302
X-RAY DIFFRACTIONf_chiral_restr0.2281030
X-RAY DIFFRACTIONf_plane_restr0.0041153
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.71830.29241420.23833540X-RAY DIFFRACTION100
2.7183-2.86170.33111430.24633553X-RAY DIFFRACTION100
2.8617-3.0410.26291420.22073533X-RAY DIFFRACTION100
3.041-3.27580.28431430.21183560X-RAY DIFFRACTION100
3.2758-3.60540.26661420.18463555X-RAY DIFFRACTION100
3.6054-4.12710.21561430.16343549X-RAY DIFFRACTION100
4.1271-5.19960.1871430.13653578X-RAY DIFFRACTION100
5.1996-83.69980.18281460.16163622X-RAY DIFFRACTION100

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