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- PDB-7a48: Crystal structure of the APH coiled-coil in complex with Nb49 -

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Basic information

Entry
Database: PDB / ID: 7a48
TitleCrystal structure of the APH coiled-coil in complex with Nb49
Components
  • APH colied-coil
  • Nanobody 49
KeywordsDE NOVO PROTEIN / coiled-coil / nanobody / antibody / protein design
Biological speciesLama glama (llama)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.547 Å
AuthorsHadzi, S.
Funding supportEuropean Union, Slovenia, 3items
OrganizationGrant numberCountry
European Research Council (ERC)787115European Union
Slovenian Research AgencyP4-0176 Slovenia
Slovenian Research AgencyP1-0201 Slovenia
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: A nanobody toolbox targeting dimeric coiled-coil modules for functionalization of designed protein origami structures.
Authors: Majerle, A. / Hadzi, S. / Aupic, J. / Satler, T. / Lapenta, F. / Strmsek, Z. / Lah, J. / Loris, R. / Jerala, R.
History
DepositionAug 19, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 5, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 11, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression / _pdbx_struct_assembly_prop.value
Revision 1.2May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nanobody 49
B: APH colied-coil


Theoretical massNumber of molelcules
Total (without water)19,4882
Polymers19,4882
Non-polymers00
Water1,72996
1
A: Nanobody 49
B: APH colied-coil

A: Nanobody 49
B: APH colied-coil


Theoretical massNumber of molelcules
Total (without water)38,9764
Polymers38,9764
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area6060 Å2
ΔGint-39 kcal/mol
Surface area15900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.580, 26.070, 54.250
Angle α, β, γ (deg.)90.000, 108.920, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody Nanobody 49


Mass: 14652.224 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#2: Protein/peptide APH colied-coil


Mass: 4835.549 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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

Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 2 M ammonium sulphate, 0.1 M sodium acetate pH 4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.547→44.735 Å / Num. obs: 18085 / % possible obs: 96.87 % / Redundancy: 3.11 % / Biso Wilson estimate: 23.47 Å2 / CC1/2: 0.996 / Rrim(I) all: 0.086 / Net I/σ(I): 7.61
Reflection shellResolution: 1.547→1.603 Å / Num. unique obs: 1644 / CC1/2: 0.722 / Rrim(I) all: 0.672 / % possible all: 89.83

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX1.12_2829refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Modeller

Resolution: 1.547→44.735 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 25.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2119 905 5.01 %
Rwork0.1787 17175 -
obs0.1805 18080 96.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 91.57 Å2 / Biso mean: 32.9294 Å2 / Biso min: 15.5 Å2
Refinement stepCycle: final / Resolution: 1.547→44.735 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1254 0 0 96 1350
Biso mean---40.68 -
Num. residues----162
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061325
X-RAY DIFFRACTIONf_angle_d0.8551800
X-RAY DIFFRACTIONf_chiral_restr0.048192
X-RAY DIFFRACTIONf_plane_restr0.005238
X-RAY DIFFRACTIONf_dihedral_angle_d2.569974
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.547-1.64360.29761410.2459266691
1.6436-1.77050.28341490.2378283698
1.7705-1.94870.27371520.2055288298
1.9487-2.23070.2091530.1807290398
2.2307-2.81030.2291520.2002288798
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.66670.9281-0.37522.54370.22162.6289-0.0738-0.34410.12280.01010.02130.009-0.09550.06710.02190.13850.0204-0.04210.1518-0.01450.093612.4942-29.183213.9456
23.67440.9504-3.38971.2282-0.95856.4543-0.26740.0807-0.234-0.1283-0.0834-0.16980.24170.26620.13070.19140.0007-0.03470.23590.00190.1743.0557-33.68282.5936
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 2 through 121)A2 - 121
2X-RAY DIFFRACTION2(chain 'B' and resid 1 through 42)B1 - 42

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