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- PDB-5u65: Camel Nanobody VHH-5 -

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Basic information

Entry
Database: PDB / ID: 5u65
TitleCamel Nanobody VHH-5
ComponentsVHH-5
KeywordsIMMUNE SYSTEM / neutralizing antibody / HIV-1 / nanobody VHH
Biological speciesCamelus dromedarius (Arabian camel)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsStanfield, R.L. / Wilson, I.A.
CitationJournal: Sci Rep / Year: 2017
Title: Selection of nanobodies with broad neutralizing potential against primary HIV-1 strains using soluble subtype C gp140 envelope trimers.
Authors: Koch, K. / Kalusche, S. / Torres, J.L. / Stanfield, R.L. / Danquah, W. / Khazanehdari, K. / von Briesen, H. / Geertsma, E.R. / Wilson, I.A. / Wernery, U. / Koch-Nolte, F. / Ward, A.B. / Dietrich, U.
History
DepositionDec 7, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: VHH-5
B: VHH-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7934
Polymers29,6012
Non-polymers1922
Water57632
1
A: VHH-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9923
Polymers14,8001
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: VHH-5


Theoretical massNumber of molelcules
Total (without water)14,8001
Polymers14,8001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.410, 48.480, 60.890
Angle α, β, γ (deg.)90.00, 114.67, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody VHH-5


Mass: 14800.268 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) / Strain (production host): HB2151
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 2.07 Å3/Da / Density % sol: 39.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 1.9M ammonium sulfate, 0.1M bicine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.3→55.3 Å / Num. obs: 10575 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Biso Wilson estimate: 21.8 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.199 / Net I/σ(I): 8.6
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.659 / Mean I/σ(I) obs: 3.5 / CC1/2: 0.927 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→55.3 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.897 / SU B: 8.684 / SU ML: 0.205 / Cross valid method: THROUGHOUT / ESU R: 0.438 / ESU R Free: 0.269 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26052 493 4.7 %RANDOM
Rwork0.20112 ---
obs0.20383 10081 98.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 22.892 Å2
Baniso -1Baniso -2Baniso -3
1-2.8 Å20 Å20.06 Å2
2---1.22 Å20 Å2
3----1.15 Å2
Refinement stepCycle: 1 / Resolution: 2.3→55.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1894 0 10 32 1936
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.021962
X-RAY DIFFRACTIONr_bond_other_d0.0020.021739
X-RAY DIFFRACTIONr_angle_refined_deg1.8341.9312666
X-RAY DIFFRACTIONr_angle_other_deg0.99233993
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.7635.039259
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.5723.90887
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.15715302
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9041514
X-RAY DIFFRACTIONr_chiral_restr0.0990.2285
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022313
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02477
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_it1.6912.171020
X-RAY DIFFRACTIONr_mcbond_other1.6892.1691019
X-RAY DIFFRACTIONr_mcangle_it2.7163.2451273
X-RAY DIFFRACTIONr_mcangle_other2.7153.2461274
X-RAY DIFFRACTIONr_scbond_it2.3592.426942
X-RAY DIFFRACTIONr_scbond_other2.2372.397934
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5953.5081379
X-RAY DIFFRACTIONr_long_range_B_refined5.06817.1162122
X-RAY DIFFRACTIONr_long_range_B_other5.06817.1062120
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 41 -
Rwork0.274 730 -
obs--99.87 %

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