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- PDB-6i2g: ALFA-tag binding nanobody (NbALFA) bound to ALFA-tag peptide. -

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Basic information

Entry
Database: PDB / ID: 6i2g
TitleALFA-tag binding nanobody (NbALFA) bound to ALFA-tag peptide.
Components
  • ALFA nanobody
  • N7P-SER-ARG-LEU-GLU-GLU-GLU-LEU-ARG-ARG-ARG-LEU-THR-GLU-LPD
KeywordsPEPTIDE BINDING PROTEIN / Nanobody / ALFA / tag
Biological speciesVicugna pacos (alpaca)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsMartinez-Carranza, M. / Stenmark, P.
CitationJournal: Nat Commun / Year: 2019
Title: The ALFA-tag is a highly versatile tool for nanobody-based bioscience applications.
Authors: Gotzke, H. / Kilisch, M. / Martinez-Carranza, M. / Sograte-Idrissi, S. / Rajavel, A. / Schlichthaerle, T. / Engels, N. / Jungmann, R. / Stenmark, P. / Opazo, F. / Frey, S.
History
DepositionNov 1, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 24, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ALFA nanobody
B: N7P-SER-ARG-LEU-GLU-GLU-GLU-LEU-ARG-ARG-ARG-LEU-THR-GLU-LPD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7174
Polymers15,5252
Non-polymers1922
Water2,126118
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint-28 kcal/mol
Surface area6720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.245, 32.379, 64.735
Angle α, β, γ (deg.)90.00, 147.22, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-383-

HOH

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Components

#1: Antibody ALFA nanobody


Mass: 13599.183 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)
#2: Protein/peptide N7P-SER-ARG-LEU-GLU-GLU-GLU-LEU-ARG-ARG-ARG-LEU-THR-GLU-LPD


Mass: 1926.183 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The N-terminal proline is blocked with an acetyl group, and the C-terminal proline is blocked with an amide group.
Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 118 / 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: 1.84 Å3/Da / Density % sol: 33.1 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: Crystal grew in a drop containing 100 nl of 100mM sodium citrate pH6.0, 2M ammonium sulphate, 4% v/v tert-Butanol, and 100 nl of the peptide-bound protein (10.1mg/ml NbALFA-ALFA peptide ...Details: Crystal grew in a drop containing 100 nl of 100mM sodium citrate pH6.0, 2M ammonium sulphate, 4% v/v tert-Butanol, and 100 nl of the peptide-bound protein (10.1mg/ml NbALFA-ALFA peptide complex, 20mM HEPES pH7.4, 100mM NaCl, 10% glycerol).

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Data collection

DiffractionMean temperature: 77 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Apr 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.5→50.36 Å / Num. obs: 17571 / % possible obs: 95.2 % / Redundancy: 5.6 % / CC1/2: 0.997 / Net I/σ(I): 12.7
Reflection shellResolution: 1.5→1.54 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VNV

5vnv


Resolution: 1.5→50.33 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.448 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.082 / ESU R Free: 0.083 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19978 865 4.9 %RANDOM
Rwork0.16522 ---
obs0.1669 16704 95.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 11.024 Å2
Baniso -1Baniso -2Baniso -3
1-1.02 Å20 Å20.21 Å2
2---0.4 Å20 Å2
3----0.22 Å2
Refinement stepCycle: 1 / Resolution: 1.5→50.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1066 0 10 118 1194
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0131112
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181004
X-RAY DIFFRACTIONr_angle_refined_deg1.8571.6691505
X-RAY DIFFRACTIONr_angle_other_deg1.5091.6082319
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0555138
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.81120.30366
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.11515187
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2271513
X-RAY DIFFRACTIONr_chiral_restr0.0830.2138
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021277
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02256
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_it1.1160.99555
X-RAY DIFFRACTIONr_mcbond_other1.1150.991556
X-RAY DIFFRACTIONr_mcangle_it1.7211.477692
X-RAY DIFFRACTIONr_mcangle_other1.7211.478693
X-RAY DIFFRACTIONr_scbond_it2.2431.261557
X-RAY DIFFRACTIONr_scbond_other2.2021.228549
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3291.763802
X-RAY DIFFRACTIONr_long_range_B_refined4.23512.1061164
X-RAY DIFFRACTIONr_long_range_B_other4.21211.8391145
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.538 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 58 -
Rwork0.188 1211 -
obs--93.93 %

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