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- PDB-9h8h: Structure of DC11 anti tau antibody Fab fragment -

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Basic information

Entry
Database: PDB / ID: 9h8h
TitleStructure of DC11 anti tau antibody Fab fragment
Components
  • DC11
  • Igk protein
KeywordsIMMUNE SYSTEM / Fab / tau protein binding
Function / homology
Function and homology information


immunoglobulin complex / adaptive immune response / extracellular region / metal ion binding / plasma membrane
Similarity search - Function
: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set ...: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Igk protein
Similarity search - Component
Biological speciesMus (mice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.331 Å
AuthorsCehlar, O. / Njemoga, S.
Funding support Slovakia, 2items
OrganizationGrant numberCountry
Other government09I03-03-V04-00623 Slovakia
Other governmentAPVV 21-0479 Slovakia
CitationJournal: To Be Published
Title: Structure of DC11 anti tau antibody Fab fragment
Authors: Cehlar, O. / Njemoga, S.
History
DepositionOct 29, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DC11
D: Igk protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3373
Polymers47,2312
Non-polymers1061
Water9,422523
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3360 Å2
ΔGint-21 kcal/mol
Surface area20160 Å2
Unit cell
Length a, b, c (Å)40.901, 88.445, 57.464
Angle α, β, γ (deg.)90.000, 94.803, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody DC11


Mass: 23031.576 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus (mice) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody Igk protein


Mass: 24198.926 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus (mice) / Gene: Igk / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: Q58EU8
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 523 / Source method: isolated from a natural source / Formula: H2O
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: 2.19 Å3/Da / Density % sol: 43.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1% MIB, 25% w/v PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.331→48.067 Å / Num. obs: 70143 / % possible obs: 90.2 % / Redundancy: 6 % / CC1/2: 0.996 / Net I/σ(I): 9.029
Reflection shellResolution: 1.331→1.432 Å / Num. unique obs: 3508 / CC1/2: 0.5694

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.331→48.067 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.964 / SU B: 2.973 / SU ML: 0.051 / Cross valid method: FREE R-VALUE / ESU R: 0.076 / ESU R Free: 0.071
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1964 3512 5.007 %
Rwork0.1452 66631 -
all0.148 --
obs-70143 75.403 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 21.224 Å2
Baniso -1Baniso -2Baniso -3
1--0.164 Å20 Å2-0.004 Å2
2--0.244 Å2-0 Å2
3----0.079 Å2
Refinement stepCycle: LAST / Resolution: 1.331→48.067 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3318 0 7 523 3848
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0123479
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163146
X-RAY DIFFRACTIONr_angle_refined_deg1.7061.8054770
X-RAY DIFFRACTIONr_angle_other_deg0.6211.7437344
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0735465
X-RAY DIFFRACTIONr_dihedral_angle_2_deg12.423511
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.41510570
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.83810138
X-RAY DIFFRACTIONr_chiral_restr0.0880.2546
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024079
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02745
X-RAY DIFFRACTIONr_nbd_refined0.2210.2580
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2230.22890
X-RAY DIFFRACTIONr_nbtor_refined0.1760.21676
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0920.21784
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.2344
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1940.224
X-RAY DIFFRACTIONr_nbd_other0.1890.275
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1130.226
X-RAY DIFFRACTIONr_mcbond_it5.682.1231758
X-RAY DIFFRACTIONr_mcbond_other5.6782.1221758
X-RAY DIFFRACTIONr_mcangle_it8.2793.8152203
X-RAY DIFFRACTIONr_mcangle_other8.2783.8152204
X-RAY DIFFRACTIONr_scbond_it7.072.4351721
X-RAY DIFFRACTIONr_scbond_other7.0692.4361722
X-RAY DIFFRACTIONr_scangle_it10.2874.3182549
X-RAY DIFFRACTIONr_scangle_other10.2854.3192550
X-RAY DIFFRACTIONr_lrange_it20.51228.5693950
X-RAY DIFFRACTIONr_lrange_other18.11726.2613802
X-RAY DIFFRACTIONr_rigid_bond_restr3.55736625
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.331-1.3660.356140.2843940.28668570.9620.9695.95010.286
1.366-1.4030.247630.25212850.25266930.9670.9620.14040.259
1.403-1.4440.311020.23224040.23564700.9410.96838.73260.239
1.444-1.4880.2361930.22233570.22363090.960.96956.26880.225
1.488-1.5370.2172440.19141260.19361180.9690.97771.42860.186
1.537-1.5910.2272550.16548750.16859440.9690.98486.30550.158
1.591-1.6510.232710.14850950.15257300.9670.98793.64750.14
1.651-1.7180.1992740.13949740.14354840.9750.98995.69660.129
1.718-1.7940.2062370.11948270.12353020.9750.99295.51110.109
1.794-1.8820.1692350.11146260.11450670.9840.99395.93450.104
1.882-1.9830.22190.11543880.11947730.9770.99396.52210.111
1.983-2.1030.1862250.12941730.13245370.9790.99196.93630.129
2.103-2.2480.2022280.1339240.13442740.9760.99197.14550.134
2.248-2.4280.1941830.1337170.13339960.9770.9997.59760.138
2.428-2.6590.1981950.13533960.13936610.9770.98998.0880.151
2.659-2.9720.1921550.14631170.14833340.9770.98798.14040.171
2.972-3.4290.2321150.15527850.15829390.9680.98698.6730.189
3.429-4.1940.1651410.14823130.1524880.9850.98798.63340.187
4.194-5.9090.172970.14618360.14819470.9850.9999.28090.192
5.909-48.0670.233660.19810190.211000.9620.97398.63640.285

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