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- PDB-9fxf: VHH variant adression natural cytotoxicity triggering receptor 3 -

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Basic information

Entry
Database: PDB / ID: 9fxf
TitleVHH variant adression natural cytotoxicity triggering receptor 3
ComponentsVHH
KeywordsIMMUNE SYSTEM / Natural killer cells / NKp30 / VHHs / humanization / molecular dynamics / Hallmark / framework residues / antigen recognition.
Function / homology12-HYDROXYDODECANOIC ACID / PHOSPHATE ION
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.067 Å
AuthorsMusil, D. / Freire, F.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Protein Sci. / Year: 2024
Title: On the humanization of VHHs: Prospective case studies, experimental and computational characterization of structural determinants for functionality.
Authors: Fernandez-Quintero, M.L. / Guarnera, E. / Musil, D. / Pekar, L. / Sellmann, C. / Freire, F. / Sousa, R.L. / Santos, S.P. / Freitas, M.C. / Bandeiras, T.M. / Silva, M.M.S. / Loeffler, J.R. / ...Authors: Fernandez-Quintero, M.L. / Guarnera, E. / Musil, D. / Pekar, L. / Sellmann, C. / Freire, F. / Sousa, R.L. / Santos, S.P. / Freitas, M.C. / Bandeiras, T.M. / Silva, M.M.S. / Loeffler, J.R. / Ward, A.B. / Harwardt, J. / Zielonka, S. / Evers, A.
History
DepositionJul 1, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 30, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: VHH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5243
Polymers14,2121
Non-polymers3112
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area320 Å2
ΔGint-1 kcal/mol
Surface area6510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.022, 34.951, 46.269
Angle α, β, γ (deg.)90.00, 108.93, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody VHH


Mass: 14212.395 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-12H / 12-HYDROXYDODECANOIC ACID


Mass: 216.317 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H24O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 2.37 Å3/Da / Density % sol: 48.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1.5 M Ammonium phosphate, 0.1 M Sodium citrate pH 5.5

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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: P14 (MX2) / Wavelength: 0.97626 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 5, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 1.067→24.522 Å / Num. obs: 37662 / % possible obs: 75.9 % / Redundancy: 6.5 % / CC1/2: 0.996 / Rpim(I) all: 0.028 / Rrim(I) all: 0.076 / Net I/σ(I): 12.4
Reflection shellResolution: 1.067→1.17 Å / Num. unique obs: 1883 / CC1/2: 0.828 / Rpim(I) all: 0.305

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Processing

Software
NameVersionClassification
BUSTER2.11.8 (23-JAN-2024)refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.067→24.52 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.947 / SU R Cruickshank DPI: 0.043 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.044 / SU Rfree Blow DPI: 0.044 / SU Rfree Cruickshank DPI: 0.043
RfactorNum. reflection% reflectionSelection details
Rfree0.2058 1942 5.16 %RANDOM
Rwork0.1927 ---
obs0.1934 37662 63.4 %-
Displacement parametersBiso mean: 12.52 Å2
Baniso -1Baniso -2Baniso -3
1--0.1743 Å20 Å2-0.339 Å2
2---0.0133 Å20 Å2
3---0.1876 Å2
Refine analyzeLuzzati coordinate error obs: 0.15 Å
Refinement stepCycle: 1 / Resolution: 1.067→24.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms915 0 19 104 1038
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0161003HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.31368HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d334SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes175HARMONIC5
X-RAY DIFFRACTIONt_it1003HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion6.09
X-RAY DIFFRACTIONt_other_torsion13.73
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion122SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1049SEMIHARMONIC4
LS refinement shellResolution: 1.07→1.13 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.3429 -4.51 %
Rwork0.253 720 -
all0.2567 754 -
obs--7.91 %
Refinement TLS params.Method: refined / Origin x: -21.657 Å / Origin y: 5.1258 Å / Origin z: 13.539 Å
111213212223313233
T-0.013 Å2-0.0051 Å2-0.0033 Å2--0.0039 Å20.0004 Å2---0.0089 Å2
L0.234 °2-0.2223 °20.1098 °2-1.1171 °2-0.0765 °2--0.2401 °2
S0.0037 Å °-0.0193 Å °-0.0019 Å °-0.029 Å °-0.0246 Å °0.0253 Å °-0.0093 Å °-0.0179 Å °0.0209 Å °
Refinement TLS groupSelection details: { A|* }

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