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- PDB-8dab: Coevolved affibody-Z domain pair LL2.c17 -

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Basic information

Entry
Database: PDB / ID: 8dab
TitleCoevolved affibody-Z domain pair LL2.c17
Components
  • Affibody LL2.IVVY
  • Immunoglobulin G-binding protein A
KeywordsPROTEIN BINDING / affibody
Function / homology
Function and homology information


IgG binding / extracellular region
Similarity search - Function
Immunoglobulin FC, subunit C / Octapeptide repeat / Octapeptide repeat / Protein A, Ig-binding domain / B domain / Lysin motif / LysM domain superfamily / LysM domain / LysM domain profile. / LysM domain ...Immunoglobulin FC, subunit C / Octapeptide repeat / Octapeptide repeat / Protein A, Ig-binding domain / B domain / Lysin motif / LysM domain superfamily / LysM domain / LysM domain profile. / LysM domain / Immunoglobulin/albumin-binding domain superfamily / YSIRK type signal peptide / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Immunoglobulin G-binding protein A
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.134 Å
AuthorsJude, K.M. / Yang, A. / Garcia, K.C.
Funding support United States, 2items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
The G. Harold and Leila Y. Mathers FoundationMF-1802-00128 United States
CitationJournal: Science / Year: 2023
Title: Deploying synthetic coevolution and machine learning to engineer protein-protein interactions.
Authors: Yang, A. / Jude, K.M. / Lai, B. / Minot, M. / Kocyla, A.M. / Glassman, C.R. / Nishimiya, D. / Kim, Y.S. / Reddy, S.T. / Khan, A.A. / Garcia, K.C.
History
DepositionJun 13, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 22, 2023Group: Data collection / Structure summary / Category: chem_comp_atom / chem_comp_bond / struct / Item: _struct.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Immunoglobulin G-binding protein A
B: Affibody LL2.IVVY


Theoretical massNumber of molelcules
Total (without water)15,5282
Polymers15,5282
Non-polymers00
Water2,666148
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, isothermal titration calorimetry, surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-10 kcal/mol
Surface area6200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.091, 35.532, 49.433
Angle α, β, γ (deg.)90.000, 115.420, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-147-

HOH

21A-171-

HOH

31B-108-

HOH

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Components

#1: Antibody Immunoglobulin G-binding protein A / IgG-binding protein A / Staphylococcal protein A / SpA


Mass: 7855.707 Da / Num. of mol.: 1 / Mutation: Q9V, G29A, I31V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: spa / Production host: Escherichia coli (E. coli) / References: UniProt: P38507
#2: Protein Affibody LL2.IVVY


Mass: 7672.605 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / 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

CrystalDensity Matthews: 1.97 Å3/Da / Density % sol: 37.53 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.2
Details: 2.3 M Amm2HPO4, 100 mM Tris pH 8.2 cryoprotected in 30% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.77488 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 8, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.77488 Å / Relative weight: 1
ReflectionResolution: 1.134→31.65 Å / Num. obs: 27318 / % possible obs: 60.77 % / Redundancy: 9.8 % / Biso Wilson estimate: 12.19 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.09152 / Rpim(I) all: 0.03031 / Rrim(I) all: 0.09654 / Net I/σ(I): 15.86
Reflection shellResolution: 1.134→1.175 Å / Redundancy: 9.4 % / Rmerge(I) obs: 4.141 / Mean I/σ(I) obs: 1.21 / Num. unique obs: 140 / CC1/2: 0.321 / CC star: 0.697 / Rpim(I) all: 1.415 / Rrim(I) all: 4.383 / % possible all: 3.1

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHENIX1.20.1_4487refinement
DIALSdata reduction
STARANISOdata scaling
PHASERphasing
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5djt

5djt


Resolution: 1.134→31.65 Å / SU ML: 0.1067 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.7765
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.1995 1528 5.6 %random selection
Rwork0.1723 25779 --
obs0.1738 27307 60.77 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.88 Å2
Refinement stepCycle: LAST / Resolution: 1.134→31.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms845 0 0 148 993
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0068905
X-RAY DIFFRACTIONf_angle_d0.82831238
X-RAY DIFFRACTIONf_chiral_restr0.0563134
X-RAY DIFFRACTIONf_plane_restr0.0094167
X-RAY DIFFRACTIONf_dihedral_angle_d12.6379352
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.134-1.170.482460.3784102X-RAY DIFFRACTION2.67
1.17-1.210.4714250.3918414X-RAY DIFFRACTION10.84
1.21-1.260.4086460.3201954X-RAY DIFFRACTION24.78
1.26-1.320.2859830.28531509X-RAY DIFFRACTION39.27
1.32-1.390.27191200.25822031X-RAY DIFFRACTION52.98
1.39-1.480.26561580.22072492X-RAY DIFFRACTION64.98
1.48-1.590.24641840.1853089X-RAY DIFFRACTION80.3
1.59-1.750.23022210.17853715X-RAY DIFFRACTION96.14
1.75-20.1912270.16243799X-RAY DIFFRACTION98.85
2-2.520.17522250.15153782X-RAY DIFFRACTION97
2.52-31.650.182330.16353892X-RAY DIFFRACTION98.19

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