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- PDB-6ru3: Crystal structure of the FP specific nanobody hFPNb1 -

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Basic information

Entry
Database: PDB / ID: 6ru3
TitleCrystal structure of the FP specific nanobody hFPNb1
ComponentshFP1Nb1
KeywordsIMMUNE SYSTEM / antibody / nanobody / single domain antibody
Biological speciesLama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.26 Å
AuthorsMazarakis, S.M.M. / Pedersen, D.V. / Laursen, N.S. / Andersen, G.R.
Funding support Denmark, 1items
OrganizationGrant numberCountry
LundbeckfondenR155-2015-2666 Denmark
Citation
Journal: Front Immunol / Year: 2019
Title: Structural Basis for Properdin Oligomerization and Convertase Stimulation in the Human Complement System.
Authors: Pedersen, D.V. / Gadeberg, T.A.F. / Thomas, C. / Wang, Y. / Joram, N. / Jensen, R.K. / Mazarakis, S.M.M. / Revel, M. / El Sissy, C. / Petersen, S.V. / Lindorff-Larsen, K. / Thiel, S. / ...Authors: Pedersen, D.V. / Gadeberg, T.A.F. / Thomas, C. / Wang, Y. / Joram, N. / Jensen, R.K. / Mazarakis, S.M.M. / Revel, M. / El Sissy, C. / Petersen, S.V. / Lindorff-Larsen, K. / Thiel, S. / Laursen, N.S. / Fremeaux-Bacchi, V. / Andersen, G.R.
#1: Journal: Febs Lett. / Year: 2019
Title: Crystal structure of peptide-bound neprilysin reveals key binding interactions.
Authors: Moss, S. / Subramanian, V. / Acharya, K.R.
History
DepositionMay 27, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 21, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: hFP1Nb1


Theoretical massNumber of molelcules
Total (without water)14,5171
Polymers14,5171
Non-polymers00
Water2,036113
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.120, 65.120, 169.260
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3
Components on special symmetry positions
IDModelComponents
11C-276-

HOH

21C-308-

HOH

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Components

#1: Antibody hFP1Nb1


Mass: 14517.155 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 2.55 Å3/Da / Density % sol: 51.7 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 13.1 % (v/v) MPD, 13.1 % PEG1000 (w/v) 13.1 % (w/v) PEG3350, 100 mM Tris Bicine pH 8.5, 33 mM CaCl2, 33 mM MgCl2, 4 % (v/v) formamide, 114 mM FOS-Choline 8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.23037→56.42 Å / Num. obs: 39873 / % possible obs: 98.3 % / Redundancy: 34 % / Biso Wilson estimate: 23 Å2 / Net I/σ(I): 32.3
Reflection shellResolution: 1.23037→1.26 Å / Num. unique obs: 2460 / % possible all: 83.4

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.26→33.85 Å / SU ML: 0.2078 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.8807
RfactorNum. reflection% reflection
Rfree0.2035 1993 5.02 %
Rwork0.1883 --
obs0.189 39728 98.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 31.72 Å2
Refinement stepCycle: LAST / Resolution: 1.26→33.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms951 0 0 113 1064
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01071010
X-RAY DIFFRACTIONf_angle_d1.1531373
X-RAY DIFFRACTIONf_chiral_restr0.0845148
X-RAY DIFFRACTIONf_plane_restr0.0066180
X-RAY DIFFRACTIONf_dihedral_angle_d18.9475374
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.23-1.260.59971090.54882196X-RAY DIFFRACTION80.96
1.26-1.30.41771400.4322560X-RAY DIFFRACTION94.04
1.3-1.330.38831430.3522669X-RAY DIFFRACTION98.22
1.33-1.380.30271420.30292700X-RAY DIFFRACTION99.68
1.38-1.430.30041370.27462719X-RAY DIFFRACTION99.79
1.43-1.480.26651500.22132731X-RAY DIFFRACTION99.97
1.48-1.550.25281490.20412715X-RAY DIFFRACTION99.93
1.55-1.630.18931460.19162734X-RAY DIFFRACTION100
1.63-1.730.19831420.18722726X-RAY DIFFRACTION100
1.73-1.870.19931470.1872750X-RAY DIFFRACTION100
1.87-2.060.17421490.17122753X-RAY DIFFRACTION99.97
2.06-2.350.17291400.17242777X-RAY DIFFRACTION100
2.35-2.960.1841430.17792798X-RAY DIFFRACTION100
2.96-33.860.20611560.18052907X-RAY DIFFRACTION99.97

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