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- PDB-6df1: Anti-phosphotyrosine antibody 4G10-4D5 Fab complexed with phospho... -

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Basic information

Entry
Database: PDB / ID: 6df1
TitleAnti-phosphotyrosine antibody 4G10-4D5 Fab complexed with phosphotyrosine peptide
Components
  • Anti-phosphotyrosine antibody 4G10-4D5 heavy chain
  • Anti-phosphotyrosine antibody 4G10-4D5 light chain
  • LEU-PTR
KeywordsIMMUNE SYSTEM / Antibody / RECOMBINATION
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 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 1.1Dec 5, 2018Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.2May 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 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: Anti-phosphotyrosine antibody 4G10-4D5 heavy chain
H: Anti-phosphotyrosine antibody 4G10-4D5 light chain
A: LEU-PTR


Theoretical massNumber of molelcules
Total (without water)52,5893
Polymers52,5893
Non-polymers00
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3870 Å2
ΔGint-35 kcal/mol
Surface area18740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.420, 98.930, 103.900
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody Anti-phosphotyrosine antibody 4G10-4D5 heavy chain


Mass: 25832.854 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): C43(DE3)
#2: Antibody Anti-phosphotyrosine antibody 4G10-4D5 light chain


Mass: 26268.637 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): C43(DE3)
#3: Protein/peptide LEU-PTR


Mass: 487.484 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 3.05 Å3/Da / Density % sol: 63.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% PEG3350, 0.2M potassium/sodium tartrate, and 0.1M Bir-tris propane

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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: Dec 10, 2016
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: 2.3→103.9 Å / Num. obs: 29265 / % possible obs: 100 % / Redundancy: 13.3 % / Biso Wilson estimate: 48.87 Å2 / Net I/σ(I): 14.5
Reflection shellResolution: 2.3→2.3677 Å

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Processing

Software
NameVersionClassification
SCALAdata scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.24data extraction
MOSFLMdata reduction
PHENIXphasing
RefinementResolution: 2.3→71.647 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.32
RfactorNum. reflection% reflection
Rfree0.2215 1635 5.59 %
Rwork0.2026 --
obs0.2036 29264 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 100.53 Å2 / Biso mean: 51.0777 Å2 / Biso min: 28.5 Å2
Refinement stepCycle: final / Resolution: 2.3→71.647 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3226 0 24 103 3353
Biso mean--42.8 47.22 -
Num. residues----433
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113308
X-RAY DIFFRACTIONf_angle_d1.2324508
X-RAY DIFFRACTIONf_chiral_restr0.065512
X-RAY DIFFRACTIONf_plane_restr0.006575
X-RAY DIFFRACTIONf_dihedral_angle_d13.5921138
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.3-2.36770.3231330.297322452378
2.3677-2.44420.34491390.300922572396
2.4442-2.53150.30621340.281922832417
2.5315-2.63290.31311360.258622422378
2.6329-2.75270.29661340.262423042438
2.7527-2.89780.27461360.25922712407
2.8978-3.07940.23391260.244222842410
3.0794-3.31720.25271410.222623092450
3.3172-3.6510.2141340.196623072441
3.651-4.17920.21271340.179623292463
4.1792-5.26510.15311420.14823342476
5.2651-71.68140.19611460.176724642610

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