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- PDB-5e2u: Structure of anti-TAU AT8 FAB in the presence of phosphopeptide -

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Basic information

Entry
Database: PDB / ID: 5e2u
TitleStructure of anti-TAU AT8 FAB in the presence of phosphopeptide
Components
  • AT8 HEAVY CHAIN
  • AT8 LIGHT CHAIN
KeywordsIMMUNE SYSTEM
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMalia, T. / Teplyakov, A.
CitationJournal: Proteins / Year: 2016
Title: Epitope mapping and structural basis for the recognition of phosphorylated tau by the anti-tau antibody AT8.
Authors: Malia, T.J. / Teplyakov, A. / Ernst, R. / Wu, S.J. / Lacy, E.R. / Liu, X. / Vandermeeren, M. / Mercken, M. / Luo, J. / Sweet, R.W. / Gilliland, G.L.
History
DepositionOct 1, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2016Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: AT8 LIGHT CHAIN
H: AT8 HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2283
Polymers48,1322
Non-polymers961
Water3,387188
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-31 kcal/mol
Surface area19150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.690, 107.380, 108.570
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11H-1165-

HOH

21H-1194-

HOH

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Components

#1: Antibody AT8 LIGHT CHAIN


Mass: 24031.848 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#2: Antibody AT8 HEAVY CHAIN


Mass: 24099.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 188 / 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: 2.87 Å3/Da / Density % sol: 57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 20% PEG 3350, 0.2 M AMMONIUM SULFATE, 15% PEG 4000, 0.2 M AMMONIUM SULFATE, 24% PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Apr 3, 2012 / Details: VARIMAX HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 21800 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Biso Wilson estimate: 40.8 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 19.5
Reflection shellResolution: 2.4→2.47 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.277 / Mean I/σ(I) obs: 5.7 / % possible all: 95.7

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Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
REFMAC5.5.0109refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 1ML8 and 3LEY

1ml8

3ley


Resolution: 2.4→15 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.904 / SU B: 6.312 / SU ML: 0.152 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.301 / ESU R Free: 0.242
RfactorNum. reflection% reflectionSelection details
Rfree0.24829 910 4.2 %RANDOM
Rwork0.186 ---
obs0.18855 20800 95.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 50.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å20 Å2
2--0.68 Å20 Å2
3----0.51 Å2
Refinement stepCycle: LAST / Resolution: 2.4→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3149 0 5 188 3342
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223207
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2151.9554387
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6355410
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.25624.32125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.17215478
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6451512
X-RAY DIFFRACTIONr_chiral_restr0.0730.2502
X-RAY DIFFRACTIONr_gen_planes_refined00.0212430
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.68622060
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.02943339
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it30.299881147
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it30.647881048
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.464 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 66 -
Rwork0.214 1415 -
obs--95.7 %

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