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- PDB-5ivo: BC2 nanobody -

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Basic information

Entry
Database: PDB / ID: 5ivo
TitleBC2 nanobody
ComponentsBC2-nanobody
KeywordsPEPTIDE BINDING PROTEIN / Nanobody / Tag / Capture / Affinity / Catenin
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesVicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 1.1Jan 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
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BC2-nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8522
Polymers14,7341
Non-polymers1181
Water72140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area370 Å2
ΔGint-13 kcal/mol
Surface area6010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.630, 47.550, 67.640
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 1.73 Å3/Da / Density % sol: 28.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: MES/imidazole, 2-Methyl-2,4-pentanediol (MPD), PEG 1000, PEG 3350, 1,6-hexanediol, 1-butanol, (RS)-1,2- propanediol, 2-propanol, 1,4-butanediol, 1,3-propanediol

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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: Aug 2, 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: 1.8→38.9 Å / Num. obs: 9931 / % possible obs: 99.9 % / Redundancy: 6.9 % / CC1/2: 0.999 / Net I/σ(I): 17.14
Reflection shellResolution: 1.8→1.85 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2X1O

2x1o


Resolution: 1.8→38.9 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2216 1192 12 %
Rwork0.1868 --
obs0.191 9930 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→38.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms881 0 8 40 929
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014935
X-RAY DIFFRACTIONf_angle_d1.4141280
X-RAY DIFFRACTIONf_dihedral_angle_d16.732327
X-RAY DIFFRACTIONf_chiral_restr0.084138
X-RAY DIFFRACTIONf_plane_restr0.006167
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8001-1.87220.31591280.2921940X-RAY DIFFRACTION99
1.8722-1.95740.25891290.2378947X-RAY DIFFRACTION100
1.9574-2.06060.24771300.1988954X-RAY DIFFRACTION100
2.0606-2.18970.20881300.1798949X-RAY DIFFRACTION100
2.1897-2.35880.22031310.1725962X-RAY DIFFRACTION100
2.3588-2.59610.23781330.2015973X-RAY DIFFRACTION100
2.5961-2.97160.20791320.1874974X-RAY DIFFRACTION100
2.9716-3.74350.20891350.1669984X-RAY DIFFRACTION100
3.7435-38.90890.20951440.17741055X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 14.6362 Å / Origin y: 1.6038 Å / Origin z: -3.8407 Å
111213212223313233
T0.114 Å20.015 Å2-0.0137 Å2-0.1161 Å2-0.0075 Å2--0.1262 Å2
L1.651 °20.1477 °2-0.8303 °2-2.6522 °20.957 °2--1.4611 °2
S0.0355 Å °-0.0695 Å °-0.2097 Å °-0.1143 Å °0.0458 Å °-0.0748 Å °0.1041 Å °0.0457 Å °0.0369 Å °
Refinement TLS groupSelection details: all

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