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- PDB-11kr: FabG1 targeting prion oligomers and fibrils -

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Basic information

Entry
Database: PDB / ID: 11kr
TitleFabG1 targeting prion oligomers and fibrils
Components
  • FabG1 heavy chain
  • FabG1 light chain
KeywordsPROTEIN BINDING / Antibody targeting prion oligomers and fibrils.
Function / homologyACETATE ION
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 Å
AuthorsBorenstein Katz, A. / Chen, P. / Fang, A. / Tang, X. / Arutyunova, E. / Dzhabrailov, I. / Rathod, V. / Lemieux, M.J. / Wille, H.
Funding support Canada, 5items
OrganizationGrant numberCountry
Other government201600012 Canada
Other government201900006 Canada
Other government212200469 Canada
Other government232403351 Canada
Other government2024N3347R Canada
CitationJournal: To Be Published
Title: Antibody targeting prion oligomers and fibrils.
Authors: Borenstein Katz, A. / Wille, H.
History
DepositionMar 2, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
J: FabG1 heavy chain
K: FabG1 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0078
Polymers48,7482
Non-polymers2596
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.754, 71.754, 89.505
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

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Antibody , 2 types, 2 molecules JK

#1: Antibody FabG1 heavy chain


Mass: 25103.125 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: p3BNC / Cell line (production host): Expi293 / Production host: Homo sapiens (human)
#2: Antibody FabG1 light chain


Mass: 23645.256 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: p3BNC / Cell line (production host): Expi293 / Production host: Homo sapiens (human) / Variant (production host): Homo sapian

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Non-polymers , 4 types, 69 molecules

#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.73 Å3/Da / Density % sol: 54.93 %
Crystal growTemperature: 293.15 K / Method: evaporation / pH: 4.5
Details: 0.2M Zinc acetate, 0.1M Sodium acetate pH 4.5, 10% PEG 3000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Nov 27, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.48→36.32 Å / Num. obs: 134886 / % possible obs: 99.18 % / Redundancy: 17.6 % / CC1/2: 0.972 / Net I/σ(I): 0.68
Reflection shellResolution: 2.48→2.62 Å / Redundancy: 7.1 % / Num. unique obs: 5233 / CC1/2: 0.00852 / CC star: 0.13 / % possible all: 94.82

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Processing

Software
NameVersionClassification
PHENIX2.0_5936refinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.48→36.32 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 28.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2426 967 5.37 %
Rwork0.1857 --
obs0.1888 17998 99.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.48→36.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3286 0 9 63 3358
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083387
X-RAY DIFFRACTIONf_angle_d0.9784615
X-RAY DIFFRACTIONf_dihedral_angle_d18.5331193
X-RAY DIFFRACTIONf_chiral_restr0.054521
X-RAY DIFFRACTIONf_plane_restr0.008589
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.48-2.620.32021280.29082307X-RAY DIFFRACTION95
2.62-2.780.31051090.24432500X-RAY DIFFRACTION100
2.78-2.990.28041340.21432447X-RAY DIFFRACTION100
3-3.290.28721800.20412409X-RAY DIFFRACTION100
3.3-3.770.22221470.19412460X-RAY DIFFRACTION100
3.77-4.750.24171310.15822459X-RAY DIFFRACTION100
4.75-36.320.19681380.15952449X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -10.55 Å / Origin y: -10.5264 Å / Origin z: 0.6787 Å
111213212223313233
T0.2299 Å20.0072 Å2-0.0091 Å2-0.1798 Å20.0365 Å2--0.27 Å2
L2.7888 °2-0.2172 °2-0.0392 °2-0.9352 °20.0857 °2--1.8043 °2
S-0.0369 Å °-0.1345 Å °0.0735 Å °-0.0184 Å °0.0282 Å °0.0389 Å °0.1537 Å °-0.0111 Å °0 Å °
Refinement TLS groupSelection details: all

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