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- PDB-5u64: Camel nanobody VHH-28 -

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Basic information

Entry
Database: PDB / ID: 5u64
TitleCamel nanobody VHH-28
ComponentsVHH-28
KeywordsIMMUNE SYSTEM / neutralizing antibody / camel vhh nanobody / HIV-1
Biological speciesCamelus dromedarius (Arabian camel)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.153 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: VHH-28


Theoretical massNumber of molelcules
Total (without water)15,0201
Polymers15,0201
Non-polymers00
Water3,009167
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.790, 76.937, 69.656
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-341-

HOH

21B-361-

HOH

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Components

#1: Antibody VHH-28


Mass: 15020.442 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelus dromedarius (Arabian camel) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 2.54 Å3/Da / Density % sol: 51.44 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 9.5 / Details: 0.1M sodium citrate, 0.1M CHES

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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: Mar 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.15→28.4 Å / Num. obs: 53677 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Biso Wilson estimate: 12.4 Å2 / CC1/2: 0.88 / Rmerge(I) obs: 0.098 / Net I/σ(I): 17.2
Reflection shellResolution: 1.15→1.17 Å / Redundancy: 4.3 % / Rmerge(I) obs: 1.54 / Mean I/σ(I) obs: 1.3 / CC1/2: 0.45 / % possible all: 97.9

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.153→28.395 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.01
RfactorNum. reflection% reflection
Rfree0.1703 2706 5.05 %
Rwork0.1454 --
obs0.1467 53637 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.153→28.395 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms978 0 0 167 1145
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0221176
X-RAY DIFFRACTIONf_angle_d1.7581630
X-RAY DIFFRACTIONf_dihedral_angle_d19.05466
X-RAY DIFFRACTIONf_chiral_restr0.125172
X-RAY DIFFRACTIONf_plane_restr0.012215
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1531-1.1740.32711250.32062546X-RAY DIFFRACTION95
1.174-1.19660.28931380.272672X-RAY DIFFRACTION99
1.1966-1.2210.22121530.2232625X-RAY DIFFRACTION100
1.221-1.24760.2021410.20572656X-RAY DIFFRACTION100
1.2476-1.27660.22341350.18612652X-RAY DIFFRACTION100
1.2766-1.30850.19881360.18232670X-RAY DIFFRACTION99
1.3085-1.34390.18241360.15752684X-RAY DIFFRACTION100
1.3439-1.38350.18371370.14252681X-RAY DIFFRACTION100
1.3835-1.42810.17021670.14142648X-RAY DIFFRACTION100
1.4281-1.47920.14071480.13092671X-RAY DIFFRACTION100
1.4792-1.53840.13191390.12392678X-RAY DIFFRACTION99
1.5384-1.60840.15011550.10542652X-RAY DIFFRACTION100
1.6084-1.69320.14241480.10862697X-RAY DIFFRACTION100
1.6932-1.79920.12881350.11652689X-RAY DIFFRACTION100
1.7992-1.93810.1291500.11632678X-RAY DIFFRACTION99
1.9381-2.13310.15281460.11562694X-RAY DIFFRACTION100
2.1331-2.44160.16361310.12912748X-RAY DIFFRACTION100
2.4416-3.07560.18441490.15272734X-RAY DIFFRACTION99
3.0756-28.40360.18051370.15842856X-RAY DIFFRACTION99

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