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- PDB-6cnr: aducanumab apo Fab -

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Basic information

Entry
Database: PDB / ID: 6cnr
Titleaducanumab apo Fab
Components
  • Aducanumab heavy chain
  • Aducanumab light chain
KeywordsIMMUNE SYSTEM / antibody Fab fragment
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsArndt, J.W.
CitationJournal: Sci Rep / Year: 2018
Title: Structural and kinetic basis for the selectivity of aducanumab for aggregated forms of amyloid-beta.
Authors: Arndt, J.W. / Qian, F. / Smith, B.A. / Quan, C. / Kilambi, K.P. / Bush, M.W. / Walz, T. / Pepinsky, R.B. / Bussiere, T. / Hamann, S. / Cameron, T.O. / Weinreb, P.H.
History
DepositionMar 8, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1May 9, 2018Group: 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.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Oct 4, 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: Aducanumab light chain
H: Aducanumab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6993
Polymers47,6032
Non-polymers961
Water4,936274
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3530 Å2
ΔGint-34 kcal/mol
Surface area19480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.311, 64.126, 67.293
Angle α, β, γ (deg.)90.00, 95.85, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11H-301-

SO4

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Components

#1: Antibody Aducanumab light chain


Mass: 23228.732 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody Aducanumab heavy chain


Mass: 24374.516 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 274 / 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: 3.27 Å3/Da / Density % sol: 62.41 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop
Details: 19% PEG 3350 in 100 mM sodium acetate, and 300 mM lithium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.987 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 10, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.09→50 Å / Num. obs: 36105 / % possible obs: 99.3 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 20.3
Reflection shellResolution: 2.09→2.16 Å / Rmerge(I) obs: 0.486

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LF3

4lf3


Resolution: 2.09→46.5 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 26.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.239 1804 5 %RANDOM
Rwork0.2108 ---
obs0.2122 36075 99.23 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.09→46.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3262 0 5 274 3541
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023335
X-RAY DIFFRACTIONf_angle_d0.6054539
X-RAY DIFFRACTIONf_dihedral_angle_d7.621982
X-RAY DIFFRACTIONf_chiral_restr0.043512
X-RAY DIFFRACTIONf_plane_restr0.004577
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.09-2.14260.29151240.2972424X-RAY DIFFRACTION92
2.1426-2.20560.27841450.27992627X-RAY DIFFRACTION100
2.2056-2.27680.34361200.29812610X-RAY DIFFRACTION99
2.2768-2.35820.29361430.25732642X-RAY DIFFRACTION100
2.3582-2.45260.30281290.25212693X-RAY DIFFRACTION100
2.4526-2.56420.29311440.24382608X-RAY DIFFRACTION100
2.5642-2.69930.28191350.24992644X-RAY DIFFRACTION100
2.6993-2.86840.29581460.23962637X-RAY DIFFRACTION100
2.8684-3.08970.29731400.23962663X-RAY DIFFRACTION100
3.0897-3.40040.26711610.2282631X-RAY DIFFRACTION100
3.4004-3.8920.19911310.19332670X-RAY DIFFRACTION100
3.892-4.90140.16661420.15962693X-RAY DIFFRACTION100
4.9014-35.64610.2191440.18272729X-RAY DIFFRACTION100

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