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- PDB-8da6: Coevolved affibody-Z domain pair LL1.c5 -

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Basic information

Entry
Database: PDB / ID: 8da6
TitleCoevolved affibody-Z domain pair LL1.c5
Components
  • (Immunoglobulin G-binding protein A) x 2
  • Affibody LL1.FIIM
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: 1.5 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.FIIM
C: Immunoglobulin G-binding protein A
D: Affibody LL1.FIIM


Theoretical massNumber of molelcules
Total (without water)31,0524
Polymers31,0524
Non-polymers00
Water2,018112
1
A: Immunoglobulin G-binding protein A
B: Affibody LL1.FIIM


Theoretical massNumber of molelcules
Total (without water)15,5392
Polymers15,5392
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1770 Å2
ΔGint-13 kcal/mol
Surface area6590 Å2
MethodPISA
2
C: Immunoglobulin G-binding protein A
D: Affibody LL1.FIIM


Theoretical massNumber of molelcules
Total (without water)15,5122
Polymers15,5122
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1690 Å2
ΔGint-11 kcal/mol
Surface area6550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.016, 42.105, 140.805
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: 7836.637 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: Protein Affibody LL1.FIIM


Mass: 7702.696 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#3: Antibody Immunoglobulin G-binding protein A / IgG-binding protein A / Staphylococcal protein A / SpA


Mass: 7809.590 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 1.77 Å3/Da / Density % sol: 30.38 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 2.4 M ammonium Sulfate 0.1 M citric acid pH 5.0 cryoprotected with sodium malonate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.77488 Å
DetectorType: DECTRIS EIGER2 XE 16M / 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: 1.5→35.8 Å / Num. obs: 36176 / % possible obs: 99.85 % / Redundancy: 12 % / Biso Wilson estimate: 28.59 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.06605 / Rpim(I) all: 0.01961 / Rrim(I) all: 0.06898 / Net I/σ(I): 20.23
Reflection shellResolution: 1.5→1.554 Å / Redundancy: 0.95 % / Rmerge(I) obs: 3.09 / Mean I/σ(I) obs: 0.95 / Num. unique obs: 3545 / CC1/2: 0.452 / CC star: 0.789 / Rpim(I) all: 0.9039 / Rrim(I) all: 3.223 / % possible all: 99.66

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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: 1.5→35.8 Å / SU ML: 0.2178 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.2242
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2507 1996 5.52 %random
Rwork0.2158 34174 --
obs0.2177 36170 99.86 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.93 Å2
Refinement stepCycle: LAST / Resolution: 1.5→35.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1798 0 0 112 1910
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00811836
X-RAY DIFFRACTIONf_angle_d0.92152486
X-RAY DIFFRACTIONf_chiral_restr0.0476268
X-RAY DIFFRACTIONf_plane_restr0.0073336
X-RAY DIFFRACTIONf_dihedral_angle_d12.3764697
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.540.40431390.39392378X-RAY DIFFRACTION99.6
1.54-1.580.38971400.3612392X-RAY DIFFRACTION99.8
1.58-1.630.39591410.3472416X-RAY DIFFRACTION99.88
1.63-1.680.30911420.33162412X-RAY DIFFRACTION99.96
1.68-1.740.33471390.27812396X-RAY DIFFRACTION99.92
1.74-1.810.30441420.2522425X-RAY DIFFRACTION99.96
1.81-1.890.27731400.24052405X-RAY DIFFRACTION99.88
1.89-1.990.27881410.25012420X-RAY DIFFRACTION99.81
1.99-2.110.2891420.23482422X-RAY DIFFRACTION100
2.11-2.280.24511420.21742446X-RAY DIFFRACTION99.85
2.28-2.510.26281430.21172449X-RAY DIFFRACTION99.85
2.51-2.870.25291450.23012477X-RAY DIFFRACTION99.89
2.87-3.610.24371450.20892496X-RAY DIFFRACTION100
3.61-35.80.21531550.18232640X-RAY DIFFRACTION99.64
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)
14.439468704844.888150505514.173514722856.180848842943.455525404846.67918441781-0.0716772508479-0.0711565872129-0.977017106530.500500901117-0.0995535640458-0.008141853148161.49491728341-0.04173871631620.03620276387790.389514414903-0.1341381155130.102872014230.32663440226-0.06687422476490.45303934357815.63581493792.1245850442894.4658111502
29.439209491951.783529744466.812175653547.021552191612.248873217165.07319431511-0.2363006043620.1067477601730.181020162814-0.2214978708670.2459532095990.363198535837-0.40450524019-0.3189962991890.01192557137690.195116514658-0.02864534067970.02677465130040.2692152807550.04113218638560.28643131739519.058962856514.127894592392.3000901876
36.443223332594.155009094814.300886653697.591741699573.295836320383.32992495874-0.09296192264560.356963721594-0.110188758009-0.01184487142780.152739083474-0.5249919684260.06933285582640.460732150701-0.08493025386020.219755180389-0.02299868534740.02008026871280.30615052875-0.01238366526170.32366022320927.00882227379.5700097797193.076893505
44.33253231134-0.218394465243-1.100945607875.29451177125-2.478484937054.613626336830.06995557370290.237508031660.537256478424-0.246313990292-0.1737417433380.0301894792988-0.2221003959710.3137950118460.222782463960.226162820517-0.00754396850608-0.03375148675650.298419708861-0.03411738287230.32451592863811.20201266649.2220726669101.390940609
52.325495583350.518151822552-2.233287522152.94220347295-3.041148314719.71976405317-0.3406397305310.08248318848520.2654427920660.2917978077310.2134319836180.206044363497-0.2900968694-0.5726803027650.09504111541080.2359543326070.05270574162710.004400697074310.340345904939-0.03233635069380.3421541691574.896840489777.5817557597105.291226694
65.873582609394.338535658824.023673344786.583225540412.977876302162.86372192851-0.2737761067260.4062250168210.165732892209-0.1543584295530.500841167065-0.720194416857-0.6428141353430.881371549244-0.2351936377650.355865977901-0.1848283352540.03574766121610.399722618531-0.0627260216190.40249160337341.29093632233.173194735479.9913469325
78.091178763155.145926085345.616918031668.681243129595.923186324995.02748817250.0967034190608-0.6436335897280.2909893540940.077598892946-0.2642999520020.0467577384383-0.454406125653-0.1657505921270.1452508051590.367881226358-0.1301065409510.04899641499440.335844154923-0.009165848299470.28325150436532.460906865130.336659724286.4906153209
84.449310612653.744951268742.286713963657.487877367253.254857235113.736945125070.317231014113-0.105162367114-0.6144355076770.5520803478130.345362887703-0.5893038162010.6993452038031.04982517002-0.6073611124780.2878180632340.02425993316560.008024644130120.40553616044-0.01643881634340.44239495644937.248575279621.513556419181.6740456674
96.309599223390.109179340247-3.377298481079.33627040585-1.800685609922.424824365070.00892940294706-0.6206877817830.6341194607870.7262166994530.3437482274431.13537249302-0.2161182416660.114993475181-0.3790243095960.370253814541-0.02757066458870.05152430679310.3628242406750.02192434290480.54795089222829.969000942237.773608370779.1740514344
109.955392601611.864347534870.5755846492551.74508579951-0.4841164557885.178871646030.27726979909-0.00182606169835-0.3458900384580.0780810941102-0.372330422947-0.0874077517760.3911931307530.009231067096420.08560469647850.3208451527130.01792859860560.046688079780.177033995502-0.02310281244140.32831663937441.424485902639.046862475269.0628238813
113.144011930840.734154897202-1.713577956810.494441861766-1.723560393126.475494857750.387416018669-0.1394826093460.529521422970.170497254528-0.08963484216320.0901044956032-0.688167788786-0.860716873599-0.3642185826580.4327763512440.04313153656130.08318068764750.27653138342-0.01579713470130.35804233746836.483733129145.070558294872.7800617355
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 3 through 18 )AA3 - 181 - 16
22chain 'A' and (resid 19 through 37 )AA19 - 3717 - 35
33chain 'A' and (resid 38 through 58 )AA38 - 5836 - 56
44chain 'B' and (resid 2 through 29 )BB2 - 291 - 28
55chain 'B' and (resid 30 through 58 )BB30 - 5829 - 57
66chain 'C' and (resid 1 through 23 )CC1 - 231 - 23
77chain 'C' and (resid 24 through 37 )CC24 - 3724 - 37
88chain 'C' and (resid 38 through 58 )CC38 - 5838 - 58
99chain 'D' and (resid 3 through 17 )DD3 - 171 - 15
1010chain 'D' and (resid 18 through 29 )DD18 - 2916 - 27
1111chain 'D' and (resid 30 through 58 )DD30 - 5828 - 56

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