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- PDB-8w9h: Crystal structure of anti-human CLEC12A antibody 50C1 -

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Basic information

Entry
Database: PDB / ID: 8w9h
TitleCrystal structure of anti-human CLEC12A antibody 50C1
Components
  • anti-human CLEC12A antibody 50C1 Fab Heavy chain
  • anti-human CLEC12A antibody 50C1 Fab Light chain
KeywordsIMMUNE SYSTEM / C-type lectin receptor / inhibitory antibody / 50C1
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMori, S. / Nagae, M. / Yamasaki, S.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)20H00505 Japan
CitationJournal: Int.Immunol. / Year: 2024
Title: Crystal structure of the complex of CLEC12A and an antibody that interferes with binding of diverse ligands.
Authors: Mori, S. / Nagae, M. / Yamasaki, S.
History
DepositionSep 5, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: 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 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: anti-human CLEC12A antibody 50C1 Fab Light chain
H: anti-human CLEC12A antibody 50C1 Fab Heavy chain
A: anti-human CLEC12A antibody 50C1 Fab Light chain
B: anti-human CLEC12A antibody 50C1 Fab Heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,66510
Polymers95,1914
Non-polymers4746
Water13,908772
1
L: anti-human CLEC12A antibody 50C1 Fab Light chain
H: anti-human CLEC12A antibody 50C1 Fab Heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9126
Polymers47,5962
Non-polymers3164
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4510 Å2
ΔGint-49 kcal/mol
Surface area19040 Å2
MethodPISA
2
A: anti-human CLEC12A antibody 50C1 Fab Light chain
B: anti-human CLEC12A antibody 50C1 Fab Heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7544
Polymers47,5962
Non-polymers1582
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3990 Å2
ΔGint-35 kcal/mol
Surface area19080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.440, 110.440, 76.242
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41
Space group name HallP4w
Symmetry operation#1: x,y,z
#2: -y,x,z+1/4
#3: y,-x,z+3/4
#4: -x,-y,z+1/2

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Components

#1: Antibody anti-human CLEC12A antibody 50C1 Fab Light chain


Mass: 23694.941 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody anti-human CLEC12A antibody 50C1 Fab Heavy chain


Mass: 23900.600 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 772 / 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: 2.46 Å3/Da / Density % sol: 50.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M Bis-tris (pH 5.5), 0.2 M ammonium sulfate, 25% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 23, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2→41.45 Å / Num. obs: 62029 / % possible obs: 100 % / Redundancy: 6.9 % / Biso Wilson estimate: 28.12 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.06 / Net I/σ(I): 10.8
Reflection shellResolution: 2→2.05 Å / Num. unique obs: 4536 / CC1/2: 0.637 / Rpim(I) all: 0.501

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→36.81 Å / SU ML: 0.2293 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.7995
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2326 2974 4.8 %
Rwork0.189 59011 -
obs0.1911 61985 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.45 Å2
Refinement stepCycle: LAST / Resolution: 2→36.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6628 0 27 772 7427
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00296815
X-RAY DIFFRACTIONf_angle_d0.62959271
X-RAY DIFFRACTIONf_chiral_restr0.04371021
X-RAY DIFFRACTIONf_plane_restr0.00851188
X-RAY DIFFRACTIONf_dihedral_angle_d6.6304929
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.030.27281360.24742755X-RAY DIFFRACTION100
2.03-2.070.32411360.2412826X-RAY DIFFRACTION100
2.07-2.110.31811380.24052767X-RAY DIFFRACTION100
2.11-2.150.25511530.23452788X-RAY DIFFRACTION99.97
2.15-2.190.27211280.23272809X-RAY DIFFRACTION99.97
2.19-2.240.30711550.2232798X-RAY DIFFRACTION99.97
2.24-2.290.2951390.22592805X-RAY DIFFRACTION100
2.29-2.350.27141260.22462825X-RAY DIFFRACTION100
2.35-2.410.26031450.2132768X-RAY DIFFRACTION100
2.41-2.480.27541310.222841X-RAY DIFFRACTION100
2.48-2.560.3011410.22592783X-RAY DIFFRACTION100
2.56-2.650.2621540.2192805X-RAY DIFFRACTION100
2.65-2.760.27231470.212793X-RAY DIFFRACTION99.93
2.76-2.880.27631450.21012801X-RAY DIFFRACTION100
2.88-3.040.24631480.19932808X-RAY DIFFRACTION99.97
3.04-3.230.23981160.18732834X-RAY DIFFRACTION99.9
3.23-3.480.23331610.17642813X-RAY DIFFRACTION100
3.48-3.820.19291420.15712828X-RAY DIFFRACTION100
3.83-4.380.17331470.14972806X-RAY DIFFRACTION100
4.38-5.510.18411550.13882848X-RAY DIFFRACTION99.97
5.52-36.810.18591310.18732910X-RAY DIFFRACTION99.7
Refinement TLS params.Method: refined / Origin x: -38.1230941238 Å / Origin y: 13.5352053773 Å / Origin z: 17.2851147223 Å
111213212223313233
T0.210535964962 Å20.0115686303116 Å20.0127082547405 Å2-0.19299848269 Å2-0.0101317273571 Å2--0.221015618221 Å2
L-6.23160770822E-5 °20.114897818424 °20.0318375055691 °2-0.032709480771 °20.00699110838109 °2--0.321447252705 °2
S0.0167017735427 Å °-0.0155541713291 Å °0.0111432574833 Å °0.023266951773 Å °-0.00802769622174 Å °-0.0555832804003 Å °0.0187931819724 Å °0.0342751653237 Å °-0.00775882296603 Å °
Refinement TLS groupSelection details: all

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