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- PDB-8da3: Coevolved affibody-Z domain pair LL1.c1 -

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Basic information

Entry
Database: PDB / ID: 8da3
TitleCoevolved affibody-Z domain pair LL1.c1
Components
  • Affibody LL1.FILF
  • 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
MALONATE ION / Immunoglobulin G-binding protein A
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.06 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.FILF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9915
Polymers15,6912
Non-polymers3003
Water2,756153
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 area1980 Å2
ΔGint-21 kcal/mol
Surface area7230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.546, 42.449, 74.288
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: 7944.822 Da / Num. of mol.: 1 / Mutation: Q9L, F13I, L17F, 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.FILF


Mass: 7745.720 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 31.13 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 2.4 M Ammonium Sulfate 0.1 M bicine pH 9.0 Cryoprotected with sodium malonate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.06→36.86 Å / Num. obs: 51100 / % possible obs: 98.53 % / Redundancy: 11.2 % / Biso Wilson estimate: 10.89 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.07684 / Rpim(I) all: 0.02358 / Rrim(I) all: 0.08051 / Net I/σ(I): 13.77
Reflection shellResolution: 1.06→1.098 Å / Redundancy: 5.5 % / Rmerge(I) obs: 1.562 / Mean I/σ(I) obs: 1.14 / Num. unique obs: 4466 / CC1/2: 0.514 / CC star: 0.824 / Rpim(I) all: 0.7217 / Rrim(I) all: 1.73 / % possible all: 87.01

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Processing

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

5djt


Resolution: 1.06→36.86 Å / SU ML: 0.0969 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.3785
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1683 2574 5.04 %
Rwork0.1469 48483 -
obs0.148 51057 98.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.83 Å2
Refinement stepCycle: LAST / Resolution: 1.06→36.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms920 0 19 153 1092
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091024
X-RAY DIFFRACTIONf_angle_d1.12711397
X-RAY DIFFRACTIONf_chiral_restr0.0736144
X-RAY DIFFRACTIONf_plane_restr0.0111189
X-RAY DIFFRACTIONf_dihedral_angle_d13.3288415
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.06-1.080.30341080.31022192X-RAY DIFFRACTION81.59
1.08-1.10.30771440.26112509X-RAY DIFFRACTION93.06
1.1-1.130.25021240.22532666X-RAY DIFFRACTION98
1.13-1.150.19791580.17942683X-RAY DIFFRACTION99.86
1.15-1.180.19871740.16362685X-RAY DIFFRACTION99.86
1.18-1.210.18081390.15172684X-RAY DIFFRACTION100
1.21-1.250.19251560.14472686X-RAY DIFFRACTION99.82
1.25-1.290.16151360.12822724X-RAY DIFFRACTION99.97
1.29-1.330.16881620.1222688X-RAY DIFFRACTION100
1.33-1.390.1391430.12482706X-RAY DIFFRACTION99.96
1.39-1.450.14961480.1312723X-RAY DIFFRACTION99.97
1.45-1.530.16071450.11042731X-RAY DIFFRACTION99.9
1.53-1.620.14951220.11082765X-RAY DIFFRACTION99.9
1.62-1.750.15541400.12042730X-RAY DIFFRACTION99.97
1.75-1.930.17931300.14212774X-RAY DIFFRACTION100
1.93-2.20.14941420.13422790X-RAY DIFFRACTION100
2.2-2.780.15781530.1442803X-RAY DIFFRACTION100
2.78-36.860.16491500.16032944X-RAY DIFFRACTION100

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