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- PDB-8qgz: NbE201 a nanobody binding human neutrophil elastase -

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Basic information

Entry
Database: PDB / ID: 8qgz
TitleNbE201 a nanobody binding human neutrophil elastase
ComponentsNbE201
KeywordsIMMUNE SYSTEM / nanobody / elastase / inhibitor / single-domain antibody
Function / homologyACETATE ION
Function and homology information
Biological speciesLama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsRedeghieri, P. / Morales-Yanez, F. / Moray, J. / Dumoulin, M. / Kerff, F.
Funding support Belgium, 2items
OrganizationGrant numberCountry
Fonds National de la Recherche Scientifique (FNRS) Belgium
Other government1710173 Belgium
CitationJournal: Protein Sci. / Year: 2024
Title: Enzymatic, structural, and biophysical characterization of a single-domain antibody (VHH) selectively and tightly inhibiting neutrophil elastase and exhibiting favorable developability properties.
Authors: Redeghieri, P. / Moray, J. / Kerff, F. / Gohy, S. / Leal, T. / Muyldermans, S. / Vanbever, R. / Morales-Yanez, F.J. / Dumoulin, M.
History
DepositionSep 6, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 25, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: NbE201
A: NbE201
C: NbE201
D: NbE201
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,5817
Polymers57,4044
Non-polymers1773
Water4,414245
1
B: NbE201
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4102
Polymers14,3511
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: NbE201
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4102
Polymers14,3511
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: NbE201


Theoretical massNumber of molelcules
Total (without water)14,3511
Polymers14,3511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: NbE201
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4102
Polymers14,3511
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.680, 88.680, 86.560
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody
NbE201


Mass: 14351.014 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Cell: B lymphocytes / Plasmid: pHEN6 / Production host: Escherichia coli (E. coli) / Strain (production host): WK6
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / 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: 2.06 Å3/Da / Density % sol: 40.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: The crystals were grown at 20oC using the sitting drop vapor diffusion method. The drop contained 0.2 uL of NbE201 at a concentration of 15 mg/mL-1 and 0.2 uL of PBS buffer pH 7.4, 10 mM ...Details: The crystals were grown at 20oC using the sitting drop vapor diffusion method. The drop contained 0.2 uL of NbE201 at a concentration of 15 mg/mL-1 and 0.2 uL of PBS buffer pH 7.4, 10 mM Na2HPO4, 1.8 mM KH2PO4, 137 mM NaCl, 2.7 mM KCl, in a cryo-protectant solution of 0.2 M Ca Acetate, 0. 1M Na Cacodylate pH 6.5 with 18% (%v/v) polyethylene glycol 8000 et 33% (%v/v) glycerol before being frozen in liquid nitrogen.

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98011 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 12, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 1.8→44.35 Å / Num. obs: 43692 / % possible obs: 97.9 % / Redundancy: 9.5 % / CC1/2: 0.994 / Net I/σ(I): 8.24
Reflection shellResolution: 1.8→1.85 Å / Num. unique obs: 3201 / CC1/2: 0.626 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→44.34 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1 / Phase error: 29.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2543 4100 4.98 %
Rwork0.2169 --
obs0.2188 43692 96.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→44.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3808 0 12 245 4065
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063958
X-RAY DIFFRACTIONf_angle_d0.8845376
X-RAY DIFFRACTIONf_dihedral_angle_d10.9992355
X-RAY DIFFRACTIONf_chiral_restr0.053576
X-RAY DIFFRACTIONf_plane_restr0.006697
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.82120.39681400.38962673X-RAY DIFFRACTION97
1.8212-1.84340.48161450.39032702X-RAY DIFFRACTION97
1.8434-1.86670.43691440.38562721X-RAY DIFFRACTION97
1.8667-1.89130.36451430.34662716X-RAY DIFFRACTION97
1.8913-1.91720.28851410.31862686X-RAY DIFFRACTION98
1.9172-1.94460.32491410.30512698X-RAY DIFFRACTION97
1.9446-1.97360.31881420.28542774X-RAY DIFFRACTION97
1.9736-2.00450.29951420.27752708X-RAY DIFFRACTION97
2.0045-2.03730.26321380.2612684X-RAY DIFFRACTION97
2.0373-2.07240.27661380.25732702X-RAY DIFFRACTION97
2.0724-2.11010.27331450.25342721X-RAY DIFFRACTION97
2.1101-2.15070.3461410.24752671X-RAY DIFFRACTION97
2.1507-2.19460.26361460.24842724X-RAY DIFFRACTION97
2.1946-2.24230.26621430.23132690X-RAY DIFFRACTION97
2.2423-2.29450.25311420.2292736X-RAY DIFFRACTION97
2.2945-2.35190.27371380.21732717X-RAY DIFFRACTION97
2.3519-2.41550.3121380.22712695X-RAY DIFFRACTION97
2.4155-2.48650.23111450.21322732X-RAY DIFFRACTION97
2.4865-2.56680.27961440.20982696X-RAY DIFFRACTION97
2.5668-2.65850.23451430.20262704X-RAY DIFFRACTION98
2.6585-2.76490.29961420.20352730X-RAY DIFFRACTION98
2.7649-2.89070.25211390.20222713X-RAY DIFFRACTION97
2.8907-3.04310.19731430.19922707X-RAY DIFFRACTION98
3.0431-3.23370.26471410.20282715X-RAY DIFFRACTION97
3.2337-3.48330.23771400.19562671X-RAY DIFFRACTION97
3.4833-3.83370.27651400.17912688X-RAY DIFFRACTION96
3.8337-4.3880.19421400.17232649X-RAY DIFFRACTION95
4.388-5.52670.19181370.17372655X-RAY DIFFRACTION95
5.5267-44.340.22361390.22232607X-RAY DIFFRACTION94

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