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- PDB-5ivn: BC2 nanobody in complex with the BC2 peptide tag -

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Basic information

Entry
Database: PDB / ID: 5ivn
TitleBC2 nanobody in complex with the BC2 peptide tag
Components
  • BC2-nanobody
  • Cadherin derived peptide
KeywordsPEPTIDE BINDING PROTEIN / Nanobody / Tag / Capture / Affinity / Catenin
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Cadherin-associated protein
Function and homology information
Biological speciesVicugna pacos (alpaca)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 Å
AuthorsBraun, M.B. / Stehle, T.
CitationJournal: Sci Rep / Year: 2016
Title: Peptides in headlock - a novel high-affinity and versatile peptide-binding nanobody for proteomics and microscopy.
Authors: Braun, M.B. / Traenkle, B. / Koch, P.A. / Emele, F. / Weiss, F. / Poetz, O. / Stehle, T. / Rothbauer, U.
History
DepositionMar 21, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 6, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 21, 2017Group: Derived calculations / Category: struct_conn / struct_sheet_range
Item: _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id ..._struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_sheet_range.beg_auth_comp_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_comp_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_comp_id / _struct_sheet_range.end_label_seq_id
Revision 1.2Jan 10, 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

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Assembly

Deposited unit
A: BC2-nanobody
B: Cadherin derived peptide


Theoretical massNumber of molelcules
Total (without water)16,2012
Polymers16,2012
Non-polymers00
Water2,396133
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint1 kcal/mol
Surface area6730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.010, 31.530, 35.880
Angle α, β, γ (deg.)90.00, 107.54, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-307-

HOH

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Components

#1: Antibody BC2-nanobody


Mass: 14734.286 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 Cadherin derived peptide


Mass: 1466.623 Da / Num. of mol.: 1 / Fragment: UNP residues 16-27 / Source method: obtained synthetically
Details: N7P is N-acetylated proline. 6E4 is amidated glutamin.
Source: (synth.) Homo sapiens (human) / References: UniProt: G9GAG7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 1.76 Å3/Da / Density % sol: 30.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: MES/imidazole, 2-Methyl-2,4-pentanediol, PEG 1000, PEG 3350, DL-Glutamatic acid monohydrate, DL-Alanine, Glycine, DL-Lysine monohydrochloride, DL-Serine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 19, 2014
RadiationMonochromator: KMC-1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 1→50.55 Å / Num. obs: 61121 / % possible obs: 99.6 % / Redundancy: 9.5 % / CC1/2: 1 / Net I/σ(I): 18.42
Reflection shellResolution: 1→1.03 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IVO

5ivo


Resolution: 1→50.55 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.977 / SU B: 0.702 / SU ML: 0.016 / Cross valid method: THROUGHOUT / ESU R: 0.022 / ESU R Free: 0.023 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.14961 3058 5 %RANDOM
Rwork0.128 ---
obs0.12908 58063 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.701 Å2
Baniso -1Baniso -2Baniso -3
1-0.46 Å2-0 Å2-0.48 Å2
2--0.17 Å20 Å2
3----0.27 Å2
Refinement stepCycle: LAST / Resolution: 1→50.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1042 0 0 133 1175
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0191192
X-RAY DIFFRACTIONr_bond_other_d0.0010.021072
X-RAY DIFFRACTIONr_angle_refined_deg1.5491.9441633
X-RAY DIFFRACTIONr_angle_other_deg1.09532478
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1825160
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.05324.06859
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.09415194
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.613158
X-RAY DIFFRACTIONr_chiral_restr0.1190.2168
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021435
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02301
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_it5.3382.992581
X-RAY DIFFRACTIONr_mcbond_other5.3432.994580
X-RAY DIFFRACTIONr_mcangle_it6.6453.366738
X-RAY DIFFRACTIONr_mcangle_other6.643.366739
X-RAY DIFFRACTIONr_scbond_it4.7474.054611
X-RAY DIFFRACTIONr_scbond_other4.7434.055612
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2994.301887
X-RAY DIFFRACTIONr_long_range_B_refined7.2668.1431413
X-RAY DIFFRACTIONr_long_range_B_other7.0867.8231366
X-RAY DIFFRACTIONr_rigid_bond_restr7.26132263
X-RAY DIFFRACTIONr_sphericity_free68.402530
X-RAY DIFFRACTIONr_sphericity_bonded15.87152327
LS refinement shellResolution: 1→1.026 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 221 -
Rwork0.351 4196 -
obs--98.11 %

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