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- PDB-8ftg: Biophysical and Structural Characterization of an Anti-Caffeine V... -

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Basic information

Entry
Database: PDB / ID: 8ftg
TitleBiophysical and Structural Characterization of an Anti-Caffeine VHH Antibody
ComponentsAnti-Caffeine VHH Antibody
KeywordsIMMUNE SYSTEM / camelid antibody / nanobody / hapten recognition / VHH / dimerization / chemically-induced dimerization (CID) system
Function / homologyCAFFEINE
Function and homology information
Biological speciesLama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.13 Å
AuthorsHorn, J.R. / Smith, C.A. / Sonneson, G.J. / Walter, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R15GM124607-01 United States
CitationJournal: Mabs / Year: 2023
Title: Molecular recognition requires dimerization of a VHH antibody.
Authors: Smith, C.A. / Sonneson, G.J. / Hoey, R.J. / Hinerman, J.M. / Sheehy, K. / Walter, R. / Herr, A.B. / Horn, J.R.
History
DepositionJan 12, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2023Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Anti-Caffeine VHH Antibody
B: Anti-Caffeine VHH Antibody
C: Anti-Caffeine VHH Antibody
D: Anti-Caffeine VHH Antibody
E: Anti-Caffeine VHH Antibody
F: Anti-Caffeine VHH Antibody
G: Anti-Caffeine VHH Antibody
H: Anti-Caffeine VHH Antibody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,33916
Polymers105,3338
Non-polymers1,0058
Water17,114950
1
A: Anti-Caffeine VHH Antibody
B: Anti-Caffeine VHH Antibody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6504
Polymers26,3332
Non-polymers3162
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2460 Å2
ΔGint-7 kcal/mol
Surface area10630 Å2
MethodPISA
2
C: Anti-Caffeine VHH Antibody
D: Anti-Caffeine VHH Antibody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5283
Polymers26,3332
Non-polymers1941
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-14 kcal/mol
Surface area10490 Å2
MethodPISA
3
E: Anti-Caffeine VHH Antibody
F: Anti-Caffeine VHH Antibody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5985
Polymers26,3332
Non-polymers2653
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2500 Å2
ΔGint-29 kcal/mol
Surface area10880 Å2
MethodPISA
4
G: Anti-Caffeine VHH Antibody
H: Anti-Caffeine VHH Antibody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5634
Polymers26,3332
Non-polymers2302
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2440 Å2
ΔGint-21 kcal/mol
Surface area10370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.136, 66.280, 68.999
Angle α, β, γ (deg.)111.620, 95.200, 90.250
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Antibody
Anti-Caffeine VHH Antibody


Mass: 13166.660 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: CDR graft into anti-RNaseA VHH Framework / Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-CFF / CAFFEINE / 3,7-DIHYDRO-1,3,7-TRIMETHYL-1H-PURINE-2,6-DIONE


Mass: 194.191 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H10N4O2 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 950 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.01 Å3/Da / Density % sol: 38.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: The VHH/caffeine complex was crystallized using the hanging-drop vapor diffusion method. The drops contained 2 microliters of the 20 mg/ml complex and 2 microliters of the well mother liquor ...Details: The VHH/caffeine complex was crystallized using the hanging-drop vapor diffusion method. The drops contained 2 microliters of the 20 mg/ml complex and 2 microliters of the well mother liquor which contained 0.1 M BIS-TRIS (pH 5.5) and 25% w/v polyethylene glycol 3,350.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 1, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.13→50 Å / Num. obs: 287785 / % possible obs: 93.81 % / Redundancy: 2.3 % / Biso Wilson estimate: 15.49 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 12.84
Reflection shellResolution: 1.131→1.171 Å / Num. unique obs: 27056 / Rpim(I) all: 0.23

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.13→27.03 Å / SU ML: 0.0911 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 17.5069
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1635 14573 5.06 %
Rwork0.1425 273186 -
obs0.1436 287759 93.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.28 Å2
Refinement stepCycle: LAST / Resolution: 1.13→27.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7278 0 67 950 8295
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00897616
X-RAY DIFFRACTIONf_angle_d1.033110338
X-RAY DIFFRACTIONf_chiral_restr0.08821105
X-RAY DIFFRACTIONf_plane_restr0.00851300
X-RAY DIFFRACTIONf_dihedral_angle_d12.58952687
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.13-1.140.24674100.21118193X-RAY DIFFRACTION83.76
1.14-1.160.234210.19558762X-RAY DIFFRACTION90.04
1.16-1.170.21554570.18618806X-RAY DIFFRACTION90.39
1.17-1.190.21644560.19118844X-RAY DIFFRACTION90.77
1.19-1.20.24115030.18548827X-RAY DIFFRACTION91.05
1.2-1.220.22614800.1798824X-RAY DIFFRACTION90.97
1.22-1.240.19824870.17348851X-RAY DIFFRACTION91.7
1.24-1.250.19764820.16288953X-RAY DIFFRACTION91.24
1.25-1.270.17864880.16288910X-RAY DIFFRACTION92.45
1.27-1.290.19314460.15948982X-RAY DIFFRACTION92.1
1.29-1.320.19144490.15569001X-RAY DIFFRACTION92.14
1.32-1.340.18824700.14579020X-RAY DIFFRACTION93.29
1.34-1.370.17245030.14199008X-RAY DIFFRACTION92.84
1.37-1.390.17764930.14129046X-RAY DIFFRACTION93.12
1.39-1.420.17194950.14249084X-RAY DIFFRACTION93.88
1.42-1.460.18085570.1429118X-RAY DIFFRACTION94.11
1.46-1.490.1854960.1429096X-RAY DIFFRACTION94.14
1.49-1.530.16514920.13289238X-RAY DIFFRACTION94.47
1.53-1.580.16764980.12859206X-RAY DIFFRACTION94.79
1.58-1.630.15844790.13099234X-RAY DIFFRACTION95.11
1.63-1.690.16994690.13679317X-RAY DIFFRACTION95.44
1.69-1.760.17294500.13739309X-RAY DIFFRACTION95.71
1.76-1.840.16914980.13829295X-RAY DIFFRACTION95.78
1.84-1.930.15514900.13879386X-RAY DIFFRACTION96.01
1.93-2.050.14965170.13069327X-RAY DIFFRACTION96.73
2.05-2.210.14635220.12969416X-RAY DIFFRACTION97.04
2.21-2.440.16165070.13619495X-RAY DIFFRACTION97.4
2.44-2.790.15925250.14389517X-RAY DIFFRACTION97.82
2.79-3.510.15695290.14279535X-RAY DIFFRACTION98.69
3.51-27.030.15675040.14599586X-RAY DIFFRACTION98.54

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