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- PDB-6dc7: Apo Fab structure of mouse monoclonal antibody 8B2 -

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Basic information

Entry
Database: PDB / ID: 6dc7
TitleApo Fab structure of mouse monoclonal antibody 8B2
Components
  • Fab heavy chain
  • Fab light chain
KeywordsIMMUNE SYSTEM / monoclonal antibody / fab / tau / phosphorylation state -specific antibody
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.901 Å
AuthorsChukwu, J.E. / Kong, X.-P.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS077239 United States
National Institutes of Health/National Institute on Aging (NIH/NIA)AG032611 United States
CitationJournal: MAbs / Year: 2019
Title: Structural characterization of monoclonal antibodies targeting C-terminal Ser404region of phosphorylated tau protein.
Authors: Chukwu, J.E. / Congdon, E.E. / Sigurdsson, E.M. / Kong, X.P.
History
DepositionMay 4, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 3, 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 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Fab light chain
H: Fab heavy chain
M: Fab light chain
I: Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)95,3384
Polymers95,3384
Non-polymers00
Water20,0691114
1
L: Fab light chain
H: Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)47,6692
Polymers47,6692
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3170 Å2
ΔGint-25 kcal/mol
Surface area19780 Å2
MethodPISA
2
M: Fab light chain
I: Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)47,6692
Polymers47,6692
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3200 Å2
ΔGint-26 kcal/mol
Surface area19900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.440, 67.474, 240.163
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11M-493-

HOH

21I-463-

HOH

31I-506-

HOH

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Components

#1: Antibody Fab light chain


Mass: 24237.729 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody Fab heavy chain


Mass: 23431.236 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1114 / 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: 2.27 Å3/Da / Density % sol: 45.83 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 20% polyethylene glycol 6000, 1 M lithium chloride, and 0.1 M citric acid pH 4.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.987 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Oct 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.9→40.3 Å / Num. obs: 65961 / % possible obs: 94.8 % / Redundancy: 1.1 % / Net I/σ(I): 14.5
Reflection shellResolution: 1.9→1.96 Å

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building
RefinementResolution: 1.901→39.918 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.45
RfactorNum. reflection% reflection
Rfree0.235 2000 3.03 %
Rwork0.1832 --
obs0.1848 65937 94.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.901→39.918 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6632 0 0 1114 7746
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076808
X-RAY DIFFRACTIONf_angle_d0.8799287
X-RAY DIFFRACTIONf_dihedral_angle_d12.2024045
X-RAY DIFFRACTIONf_chiral_restr0.0581046
X-RAY DIFFRACTIONf_plane_restr0.0051173
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9007-1.94820.26661280.19924123X-RAY DIFFRACTION87
1.9482-2.00090.2611350.20294285X-RAY DIFFRACTION90
2.0009-2.05970.2791340.20454312X-RAY DIFFRACTION91
2.0597-2.12620.28691370.20184366X-RAY DIFFRACTION92
2.1262-2.20220.2591380.19334399X-RAY DIFFRACTION92
2.2022-2.29040.31841380.19984423X-RAY DIFFRACTION93
2.2904-2.39460.2741410.20394489X-RAY DIFFRACTION94
2.3946-2.52080.2681420.21124561X-RAY DIFFRACTION95
2.5208-2.67870.29791450.21034652X-RAY DIFFRACTION97
2.6787-2.88550.24161480.20734713X-RAY DIFFRACTION99
2.8855-3.17580.23771500.19084821X-RAY DIFFRACTION99
3.1758-3.63510.22131520.17224836X-RAY DIFFRACTION100
3.6351-4.57870.19331530.14784906X-RAY DIFFRACTION100
4.5787-39.92710.18491590.16595051X-RAY DIFFRACTION98

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