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- PDB-8e1c: Crystal Structure of Nanobody VHH222 Specific for PA14 Cif -

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Entry
Database: PDB / ID: 8e1c
TitleCrystal Structure of Nanobody VHH222 Specific for PA14 Cif
ComponentsNanobody VHH222
KeywordsIMMUNE SYSTEM / Pseudomonas aeruginosa / nanobody VHH / immunoglobulin domain / CFTR inhibitory factor (Cif)
Biological speciesVicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSimard, A.R. / Taher, N.M. / Stuut, S.E. / 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 VHH222 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nanobody VHH222


Theoretical massNumber of molelcules
Total (without water)13,5311
Polymers13,5311
Non-polymers00
Water1,02757
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)58.006, 58.006, 75.935
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-213-

HOH

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Components

#1: Antibody Nanobody VHH222


Mass: 13531.143 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Plasmid: pET16b / Details (production host): N-term 10X His-SUMO fusion / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): DE3 RIL
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O

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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: 2.73 Å3/Da / Density % sol: 54.87 %
Crystal growTemperature: 292.8 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 100 mM succinic acid/sodium phosphate monobasic/glycine 2:7:7 (SPG) pH 6.0, 25% (w/v) PEG1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.978636 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 29, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978636 Å / Relative weight: 1
ReflectionResolution: 1.9→41.9 Å / Num. obs: 12038 / % possible obs: 99.48 % / Redundancy: 9.5 % / Biso Wilson estimate: 35.72 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.07468 / Rpim(I) all: 0.02545 / Rrim(I) all: 0.07902 / Net I/σ(I): 16.76
Reflection shellResolution: 1.9→1.968 Å / Redundancy: 7.6 % / Rmerge(I) obs: 1.286 / Mean I/σ(I) obs: 1.58 / Num. unique obs: 1142 / CC1/2: 0.838 / CC star: 0.955 / Rpim(I) all: 0.4838 / Rrim(I) all: 1.379 / % possible all: 97.35

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX1.20.1_4487refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EZJ

3ezj


Resolution: 1.9→41.9 Å / SU ML: 0.2361 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 30.2802
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Details: Positive electron-density peaks are observed where residues 104:106 of Chain A would be located, but the placement of main-chain atoms could not be resolved.
RfactorNum. reflection% reflection
Rfree0.2242 598 4.98 %
Rwork0.212 11415 -
obs0.2126 12013 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.92 Å2
Refinement stepCycle: LAST / Resolution: 1.9→41.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms881 0 0 57 938
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098894
X-RAY DIFFRACTIONf_angle_d0.81851208
X-RAY DIFFRACTIONf_chiral_restr0.0626136
X-RAY DIFFRACTIONf_plane_restr0.0031156
X-RAY DIFFRACTIONf_dihedral_angle_d13.9787321
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-2.090.33961480.28782755X-RAY DIFFRACTION98.47
2.09-2.390.2631540.23542825X-RAY DIFFRACTION99.7
2.39-3.020.29531500.24622847X-RAY DIFFRACTION99.93
3.02-41.90.18141460.18842988X-RAY DIFFRACTION99.84

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