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- PDB-8e1b: Crystal Structure of Nanobody VHH108 Specific for PA14 Cif -

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Basic information

Entry
Database: PDB / ID: 8e1b
TitleCrystal Structure of Nanobody VHH108 Specific for PA14 Cif
ComponentsNanobody VHH108
KeywordsIMMUNE SYSTEM / Pseudomonas aeruginosa / nanobody VHH / immunoglobulin domain / CFTR inhibitory factor (Cif)
Biological speciesVicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsSimard, A.R. / Taher, N.M. / Mishra, A.K. / Madden, D.R.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01-AI091699 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)P30-DK117469 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20-GM113132 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)T32AI007519 United States
Cystic Fibrosis FoundationSTANTO19R0 United States
Citation
Journal: To Be Published
Title: Crystal Structure of Nanobody VHH108 Specific for PA14 Cif
Authors: Simard, A.R. / Madden, D.R.
#1: Journal: Anal Chim Acta / Year: 2019
Title: Nanobody-based binding assay for the discovery of potent inhibitors of CFTR inhibitory factor (Cif).
Authors: Vasylieva, N. / Kitamura, S. / Dong, J. / Barnych, B. / Hvorecny, K.L. / Madden, D.R. / Gee, S.J. / Wolan, D.W. / Morisseau, C. / Hammock, B.D.
History
DepositionAug 10, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 4, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nanobody VHH108


Theoretical massNumber of molelcules
Total (without water)16,2931
Polymers16,2931
Non-polymers00
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)30.871, 112.147, 33.198
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: Antibody Nanobody VHH108


Mass: 16293.013 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Plasmid: pComb3X / Production host: Escherichia coli BL21 (bacteria)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O
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: 1.77 Å3/Da / Density % sol: 30.38 %
Crystal growTemperature: 292.8 K / Method: vapor diffusion, sitting drop / Details: 200 mM sodium thiocyanate, 20% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.920099 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jan 22, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.920099 Å / Relative weight: 1
ReflectionResolution: 1.65→33.2 Å / Num. obs: 14566 / % possible obs: 99.92 % / Redundancy: 6.3 % / Biso Wilson estimate: 30.8 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.05386 / Rpim(I) all: 0.02353 / Rrim(I) all: 0.05892 / Net I/σ(I): 15.12
Reflection shellResolution: 1.65→1.709 Å / Redundancy: 5.4 % / Rmerge(I) obs: 1.192 / Mean I/σ(I) obs: 1.14 / Num. unique obs: 1430 / CC1/2: 0.623 / CC star: 0.876 / Rpim(I) all: 0.5613 / Rrim(I) all: 1.319 / % possible all: 99.93

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4jvp

4jvp


Resolution: 1.65→33.2 Å / SU ML: 0.275 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.8562
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Details: The boundaries for stretches of missing residues were determined using a composite omit map with a one-sigma cutoff unless otherwise stated. Positive electron-density peaks are observed ...Details: The boundaries for stretches of missing residues were determined using a composite omit map with a one-sigma cutoff unless otherwise stated. Positive electron-density peaks are observed where residues 74:76 of Chain A would be located, but the placement of main-chain atoms could not be resolved. Atoms modeled with zero occupancy could not be placed with confidence and were selected for zero-occupancy flagging after manual inspection of the 2Fo-Fc map at a 0.5-sigma cutoff. Although the correlation is low, residues 30 and 103 in Chain A have reasonable concordance with the 2Fo-Fc map, are not rotamer outliers, and are devoid of clashes with neighboring atoms.
RfactorNum. reflection% reflection
Rfree0.2148 691 4.74 %
Rwork0.2115 13873 -
obs0.2117 14564 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.05 Å2
Refinement stepCycle: LAST / Resolution: 1.65→33.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms864 0 0 53 917
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0069908
X-RAY DIFFRACTIONf_angle_d0.83631229
X-RAY DIFFRACTIONf_chiral_restr0.0587137
X-RAY DIFFRACTIONf_plane_restr0.0073160
X-RAY DIFFRACTIONf_dihedral_angle_d14.138327
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.780.39341310.35752713X-RAY DIFFRACTION99.93
1.78-1.960.27911380.23182736X-RAY DIFFRACTION100
1.96-2.240.23651390.21922733X-RAY DIFFRACTION100
2.24-2.820.25921410.22592771X-RAY DIFFRACTION99.93
2.82-33.20.17651420.19342920X-RAY DIFFRACTION99.77

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