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- PDB-5m7q: Engineering the Thermostability of Nanobodies - NbD2 -

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Basic information

Entry
Database: PDB / ID: 5m7q
TitleEngineering the Thermostability of Nanobodies - NbD2
ComponentsNanobody NbD2
KeywordsIMMUNE SYSTEM / Nanobody / VHH / variable domain / Camelids
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesCamelus dromedarius (Arabian camel)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSoler, N. / Kunz, P. / Muyldermans, S.
CitationJournal: To be published
Title: Engineering the Thermostability of Nanobodies
Authors: Kunz, P. / Flock, T. / Soler, N. / Zaiss, M. / Vincke, C. / Sterckx, Y. / Muyldermans, S. / Kastelic, D. / Hoheisel, J.
History
DepositionOct 28, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Nanobody NbD2
A: Nanobody NbD2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,58213
Polymers30,0932
Non-polymers48911
Water2,972165
1
B: Nanobody NbD2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3097
Polymers15,0471
Non-polymers2626
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Nanobody NbD2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2736
Polymers15,0471
Non-polymers2275
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-75 kcal/mol
Surface area13130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.058, 49.058, 225.735
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Nanobody NbD2


Mass: 15046.653 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelus dromedarius (Arabian camel) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 2.57 Å3/Da / Density % sol: 52.22 %
Crystal growTemperature: 290.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM MES, pH 6.5, 1.6 M magnesium sulfate heptahydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97921 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 1.8→25.69 Å / Num. obs: 30508 / % possible obs: 100 % / Redundancy: 7.7 % / CC1/2: 0.999 / Net I/σ(I): 11.7
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.479 / Mean I/σ(I) obs: 2.5 / CC1/2: 0.775 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4W6X

4w6x


Resolution: 1.8→25.69 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.934 / SU B: 3.092 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.122 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24856 1437 4.7 %RANDOM
Rwork0.19589 ---
obs0.1984 28992 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 28.887 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20.12 Å20 Å2
2--0.25 Å2-0 Å2
3----0.8 Å2
Refinement stepCycle: 1 / Resolution: 1.8→25.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1907 0 19 165 2091
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.021966
X-RAY DIFFRACTIONr_bond_other_d0.0060.021801
X-RAY DIFFRACTIONr_angle_refined_deg2.0471.9472668
X-RAY DIFFRACTIONr_angle_other_deg1.09434132
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2525250
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.61623.05985
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.7115308
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6781516
X-RAY DIFFRACTIONr_chiral_restr0.1320.2282
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212280
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02476
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.1022.5821003
X-RAY DIFFRACTIONr_mcbond_other3.0882.5791002
X-RAY DIFFRACTIONr_mcangle_it4.3433.851252
X-RAY DIFFRACTIONr_mcangle_other4.3413.8531253
X-RAY DIFFRACTIONr_scbond_it3.8463.022963
X-RAY DIFFRACTIONr_scbond_other3.8393.004955
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.984.3231405
X-RAY DIFFRACTIONr_long_range_B_refined7.92721.9052255
X-RAY DIFFRACTIONr_long_range_B_other7.87721.5662203
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 85 -
Rwork0.264 2112 -
obs--100 %

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