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- PDB-8da7: Coevolved affibody-Z domain pair LL1.c6 -

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Basic information

Entry
Database: PDB / ID: 8da7
TitleCoevolved affibody-Z domain pair LL1.c6
Components
  • Immunoglobulin G-binding protein A
  • affibody LL1.FIFV
KeywordsPROTEIN BINDING / affibody
Function / homology
Function and homology information


IgG binding / extracellular region
Similarity search - Function
Octapeptide repeat / Octapeptide repeat / Protein A, Ig-binding domain / B domain / LysM domain superfamily / Lysin motif / LysM domain / LysM domain profile. / LysM domain / Immunoglobulin/albumin-binding domain superfamily ...Octapeptide repeat / Octapeptide repeat / Protein A, Ig-binding domain / B domain / LysM domain superfamily / Lysin motif / 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
Similarity search - Domain/homology
MALONATE ION / Immunoglobulin G-binding protein A
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.02 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

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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 LL1.FIFV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7193
Polymers15,6162
Non-polymers1021
Water2,972165
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry, gel filtration, surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-10 kcal/mol
Surface area7240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.617, 42.380, 74.222
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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


Mass: 7911.812 Da / Num. of mol.: 1 / Mutation: Q9L, F13I, G29A, I31F
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 LL1.FIFV


Mass: 7704.648 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: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 1.79 Å3/Da / Density % sol: 31.42 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 2.5 M AmmSO4, 100 mM tris pH 8.5 cryoprotected with Na malonate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.77487 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jan 18, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.77487 Å / Relative weight: 1
ReflectionResolution: 1.02→27.91 Å / Num. obs: 57264 / % possible obs: 98.75 % / Redundancy: 8.1 % / Biso Wilson estimate: 13.13 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.06462 / Rpim(I) all: 0.02412 / Rrim(I) all: 0.06915 / Net I/σ(I): 12.91
Reflection shellResolution: 1.02→1.056 Å / Redundancy: 8.4 % / Rmerge(I) obs: 2.47 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 5584 / CC1/2: 0.456 / CC star: 0.791 / Rpim(I) all: 0.8953 / Rrim(I) all: 2.631 / % possible all: 97.38

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Processing

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

5djt


Resolution: 1.02→27.27 Å / SU ML: 0.1291 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.0981
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.1828 2873 5.02 %random
Rwork0.1601 54356 --
obs0.1612 57229 98.75 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.71 Å2
Refinement stepCycle: LAST / Resolution: 1.02→27.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms914 0 7 165 1086
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0159975
X-RAY DIFFRACTIONf_angle_d1.41991330
X-RAY DIFFRACTIONf_chiral_restr0.089145
X-RAY DIFFRACTIONf_plane_restr0.0108179
X-RAY DIFFRACTIONf_dihedral_angle_d13.5586384
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.02-1.040.42741370.38222498X-RAY DIFFRACTION97.02
1.04-1.050.37871080.32922559X-RAY DIFFRACTION97.84
1.05-1.070.28811300.28492534X-RAY DIFFRACTION98.3
1.07-1.090.26411400.25872541X-RAY DIFFRACTION98.1
1.09-1.120.22081280.23892541X-RAY DIFFRACTION97.77
1.12-1.140.26031320.21792549X-RAY DIFFRACTION98.57
1.14-1.170.2241510.20772535X-RAY DIFFRACTION98.9
1.17-1.20.20731360.18982552X-RAY DIFFRACTION97.92
1.2-1.230.22911620.17192534X-RAY DIFFRACTION98.65
1.23-1.270.20741450.16762554X-RAY DIFFRACTION98.72
1.27-1.310.191410.15052565X-RAY DIFFRACTION99.12
1.31-1.350.15331470.14752592X-RAY DIFFRACTION99.31
1.35-1.410.17811240.15592595X-RAY DIFFRACTION99.41
1.41-1.470.19041340.142606X-RAY DIFFRACTION99.24
1.47-1.550.14881410.12932602X-RAY DIFFRACTION99.46
1.55-1.650.15771480.1262554X-RAY DIFFRACTION97.97
1.65-1.770.18521300.13522636X-RAY DIFFRACTION99.53
1.77-1.950.19311250.14782655X-RAY DIFFRACTION99.93
1.95-2.230.1481260.13292691X-RAY DIFFRACTION99.93
2.23-2.810.15111370.15242687X-RAY DIFFRACTION99.93
2.81-27.270.18971510.16752776X-RAY DIFFRACTION98.25

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