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- PDB-8da5: Coevolved affibody-Z domain pair LL1.c4 -

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Basic information

Entry
Database: PDB / ID: 8da5
TitleCoevolved affibody-Z domain pair LL1.c4
Components
  • (Immunoglobulin G-binding protein ...) x 2
  • (affibody LL1. ...) x 2
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 / Lysin motif / LysM domain superfamily / LysM domain / LysM domain profile. / LysM domain / Immunoglobulin/albumin-binding domain superfamily ...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
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 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
C: Immunoglobulin G-binding protein A
B: affibody LL1.FIVM
D: affibody LL1.FIVM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3355
Polymers31,2434
Non-polymers921
Water6,828379
1
A: Immunoglobulin G-binding protein A
B: affibody LL1.FIVM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6723
Polymers15,5802
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-12 kcal/mol
Surface area7320 Å2
MethodPISA
2
C: Immunoglobulin G-binding protein A
D: affibody LL1.FIVM


Theoretical massNumber of molelcules
Total (without water)15,6632
Polymers15,6632
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-14 kcal/mol
Surface area7240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.612, 41.153, 160.108
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

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Affibody LL1. ... , 2 types, 2 molecules BD

#3: Protein affibody LL1.FIVM


Mass: 7715.715 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)
#4: Protein affibody LL1.FIVM


Mass: 7743.769 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)

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Antibody , 2 types, 2 molecules AC

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


Mass: 7864.690 Da / Num. of mol.: 1 / Mutation: Q9F, 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: Antibody Immunoglobulin G-binding protein A / IgG-binding protein A / Staphylococcal protein A / SpA


Mass: 7918.783 Da / Num. of mol.: 1 / Mutation: Q9F, 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

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Non-polymers , 2 types, 380 molecules

#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 379 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.04 Å3/Da / Density % sol: 39.58 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 2.3 M AmmPO4, 100 mM Tris pH 8.5 cryoprotected with 30% glycerol

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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→40.03 Å / Num. obs: 138513 / % possible obs: 99.11 % / Redundancy: 12.7 % / Biso Wilson estimate: 13.1 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.07674 / Rpim(I) all: 0.02219 / Rrim(I) all: 0.07997 / Net I/σ(I): 10.75
Reflection shellResolution: 1→1.036 Å / Redundancy: 12.6 % / Rmerge(I) obs: 2.947 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 13660 / CC1/2: 0.657 / CC star: 0.891 / Rpim(I) all: 0.8613 / Rrim(I) all: 3.073 / % possible all: 98.87

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Processing

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

5djt


Resolution: 1→40.03 Å / SU ML: 0.1498 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.0658
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1912 6854 4.98 %
Rwork0.1677 130718 -
obs0.1689 137572 99.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.7 Å2
Refinement stepCycle: LAST / Resolution: 1→40.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1893 0 6 379 2278
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0161995
X-RAY DIFFRACTIONf_angle_d1.41892714
X-RAY DIFFRACTIONf_chiral_restr0.0888289
X-RAY DIFFRACTIONf_plane_restr0.0104365
X-RAY DIFFRACTIONf_dihedral_angle_d12.3212781
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1-1.010.46142500.43194234X-RAY DIFFRACTION97.65
1.01-1.020.37472060.38564347X-RAY DIFFRACTION99.8
1.02-1.040.38762150.3514256X-RAY DIFFRACTION98.11
1.04-1.050.35252310.34664244X-RAY DIFFRACTION97.86
1.05-1.060.35942320.33744257X-RAY DIFFRACTION98.1
1.06-1.080.38042330.30924281X-RAY DIFFRACTION98.47
1.08-1.090.31992370.29374245X-RAY DIFFRACTION98.53
1.09-1.110.32360.27664339X-RAY DIFFRACTION98.6
1.11-1.130.29742070.26084286X-RAY DIFFRACTION98.68
1.13-1.140.23922300.23834309X-RAY DIFFRACTION99.04
1.14-1.160.25932330.22224296X-RAY DIFFRACTION98.8
1.16-1.190.25662180.21664285X-RAY DIFFRACTION98.49
1.19-1.210.20942220.2124278X-RAY DIFFRACTION97.11
1.21-1.230.21842160.19184291X-RAY DIFFRACTION99.01
1.23-1.260.19182090.1774350X-RAY DIFFRACTION99.04
1.26-1.290.19732310.1714375X-RAY DIFFRACTION99.1
1.29-1.320.19242170.16454319X-RAY DIFFRACTION99.36
1.32-1.360.21881810.17064385X-RAY DIFFRACTION99.56
1.36-1.40.21332260.16734397X-RAY DIFFRACTION99.7
1.4-1.440.18352140.15224403X-RAY DIFFRACTION99.7
1.44-1.490.16332580.1324342X-RAY DIFFRACTION99.67
1.49-1.550.17252510.12284372X-RAY DIFFRACTION99.76
1.55-1.620.14932210.12734374X-RAY DIFFRACTION99.14
1.62-1.710.13572270.13264403X-RAY DIFFRACTION99.19
1.71-1.820.1832280.14624428X-RAY DIFFRACTION99.96
1.82-1.960.17132270.14434453X-RAY DIFFRACTION99.98
1.96-2.150.16592440.14194444X-RAY DIFFRACTION99.83
2.15-2.470.16812630.13724447X-RAY DIFFRACTION99.85
2.47-3.110.19092310.15764534X-RAY DIFFRACTION99.73
3.11-40.030.17842600.16994744X-RAY DIFFRACTION99.92

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