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- PDB-6df0: anti-phosphotyrosine antibody 4G10-4D5 Fab complexed with sulfate -

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Basic information

Entry
Database: PDB / ID: 6df0
Titleanti-phosphotyrosine antibody 4G10-4D5 Fab complexed with sulfate
Components
  • 4G10-4D5 Antibody Light chain
  • 4G10-4D5 Antibody heavy chain
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: 2.3 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 1.1May 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 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: 4G10-4D5 Antibody Light chain
H: 4G10-4D5 Antibody heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8093
Polymers54,7132
Non-polymers961
Water3,567198
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3520 Å2
ΔGint-43 kcal/mol
Surface area18530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.900, 98.900, 207.364
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11L-405-

HOH

21H-436-

HOH

31H-490-

HOH

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Components

#1: Antibody 4G10-4D5 Antibody Light chain


Mass: 26829.830 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Antibody 4G10-4D5 Antibody heavy chain


Mass: 27883.322 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / 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: 2.68 Å3/Da / Density % sol: 54.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% PEG4000, 0.2M ammonium sulfate, and 0.1M sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11583 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 31, 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: 1.11583 Å / Relative weight: 1
ReflectionResolution: 1.82→85.65 Å / Num. obs: 27809 / % possible obs: 100 % / Redundancy: 17.6 % / Biso Wilson estimate: 30.81 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.017 / Rrim(I) all: 0.072 / Net I/σ(I): 22.7
Reflection shellResolution: 1.82→1.86 Å / Redundancy: 18 % / Rmerge(I) obs: 0.695 / Num. unique obs: 3136 / CC1/2: 0.973 / Rpim(I) all: 0.168 / Rrim(I) all: 0.715 / % possible all: 100

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Processing

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

1bj1


Resolution: 2.3→85.65 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 25.73
RfactorNum. reflection% reflection
Rfree0.2439 1310 4.78 %
Rwork0.2003 --
obs0.2024 27427 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→85.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3175 0 5 198 3378
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083262
X-RAY DIFFRACTIONf_angle_d0.9554450
X-RAY DIFFRACTIONf_dihedral_angle_d3.4581918
X-RAY DIFFRACTIONf_chiral_restr0.062503
X-RAY DIFFRACTIONf_plane_restr0.005568
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3001-2.39220.36231430.24632802X-RAY DIFFRACTION100
2.3922-2.50110.28691320.22632849X-RAY DIFFRACTION100
2.5011-2.63290.29831390.22442841X-RAY DIFFRACTION100
2.6329-2.79790.29211700.22882833X-RAY DIFFRACTION100
2.7979-3.01390.2661300.22242885X-RAY DIFFRACTION100
3.0139-3.31730.24451340.21542893X-RAY DIFFRACTION100
3.3173-3.79730.25081600.19852907X-RAY DIFFRACTION100
3.7973-4.78410.19821410.16072960X-RAY DIFFRACTION100
4.7841-85.70910.19791610.18823147X-RAY DIFFRACTION100

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