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- PDB-8da4: Coevolved affibody-Z domain pair LL1.c2 -

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Basic information

Entry
Database: PDB / ID: 8da4
TitleCoevolved affibody-Z domain pair LL1.c2
Components
  • Affibody LL1.FIVM
  • Immunoglobulin G-binding protein A
  • affibody LL1.FIVM
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: 1.92 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.FIVM
C: Immunoglobulin G-binding protein A
D: affibody LL1.FIVM
E: Immunoglobulin G-binding protein A
F: affibody LL1.FIVM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5977
Polymers46,5016
Non-polymers961
Water1,946108
1
A: Immunoglobulin G-binding protein A
B: Affibody LL1.FIVM


Theoretical massNumber of molelcules
Total (without water)15,5182
Polymers15,5182
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1430 Å2
ΔGint-11 kcal/mol
Surface area6780 Å2
MethodPISA
2
C: Immunoglobulin G-binding protein A
D: affibody LL1.FIVM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5873
Polymers15,4912
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-25 kcal/mol
Surface area6620 Å2
MethodPISA
3
E: Immunoglobulin G-binding protein A
F: affibody LL1.FIVM


Theoretical massNumber of molelcules
Total (without water)15,4912
Polymers15,4912
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-11 kcal/mol
Surface area6320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.449, 72.449, 181.469
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11B-108-

HOH

21B-124-

HOH

31F-114-

HOH

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Components

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


Mass: 7802.622 Da / Num. of mol.: 3 / 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.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)
#3: Protein affibody LL1.FIVM


Mass: 7688.669 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)
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 2.56 Å3/Da / Density % sol: 51.96 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 2.5 M AmmSO4, 0.1 M NaOAc pH 4.6 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: 1.92→49.3 Å / Num. obs: 37848 / % possible obs: 99.72 % / Redundancy: 24.7 % / Biso Wilson estimate: 42.6 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.1035 / Rpim(I) all: 0.02097 / Rrim(I) all: 0.1056 / Net I/σ(I): 15.82
Reflection shellResolution: 1.92→1.989 Å / Redundancy: 17.4 % / Rmerge(I) obs: 3.227 / Num. unique obs: 3691 / CC1/2: 0.464 / CC star: 0.796 / Rpim(I) all: 0.7771 / Rrim(I) all: 3.324 / % possible all: 99.41

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Processing

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

5djt


Resolution: 1.92→49.3 Å / SU ML: 0.2835 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.4186
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2473 1856 4.91 %
Rwork0.2034 35920 -
obs0.2055 37776 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.42 Å2
Refinement stepCycle: LAST / Resolution: 1.92→49.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2602 0 5 108 2715
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142676
X-RAY DIFFRACTIONf_angle_d1.29523635
X-RAY DIFFRACTIONf_chiral_restr0.067395
X-RAY DIFFRACTIONf_plane_restr0.0092493
X-RAY DIFFRACTIONf_dihedral_angle_d14.77641016
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.92-1.970.40491260.3412690X-RAY DIFFRACTION98.46
1.97-2.030.36371340.32992705X-RAY DIFFRACTION99.96
2.03-2.090.32471510.30522700X-RAY DIFFRACTION99.72
2.09-2.170.31711350.26852724X-RAY DIFFRACTION99.65
2.17-2.260.32061400.24462719X-RAY DIFFRACTION99.76
2.26-2.360.26461470.22282714X-RAY DIFFRACTION99.51
2.36-2.480.30921460.22662740X-RAY DIFFRACTION99.79
2.48-2.640.28121430.2362736X-RAY DIFFRACTION99.76
2.64-2.840.26681360.23222760X-RAY DIFFRACTION99.72
2.84-3.130.30061170.22152801X-RAY DIFFRACTION99.97
3.13-3.580.24211600.19752792X-RAY DIFFRACTION99.9
3.58-4.510.21731500.16352838X-RAY DIFFRACTION99.83
4.51-49.30.20041710.17533001X-RAY DIFFRACTION99.81
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)
13.96055024588-1.19720915911-1.259806185122.10067633233-0.8600503191283.34098621350.159573097562-0.271860408770.297286040744-0.4110239523080.629199442443-0.571257444812-0.7750051669241.03356233422-0.6556680536640.657948933492-0.2091337116730.08329755253760.556099643132-0.2623651245920.52765279522331.756487326642.792521834998.7871427826
21.568565498561.009647462370.9227025712933.096443163421.099093617474.54701296186-0.1968626552730.4829247779380.0621260402601-0.7990882467070.432909443979-0.0158370695283-1.35088735975-0.043077293551-0.2642360766161.00941011364-0.1390276385440.1492963581060.3564051080580.02539949328950.46697187024423.934082035146.593704445388.9778543892
30.2064738863270.512088459850.1297188000131.617314321760.05400162397420.271475213915-0.02433428907340.248500283288-0.0571094476168-0.5517135978690.354256314972-0.436542761862-0.6891233294750.238273086010.1044988846911.33616248397-0.6728582412320.4053899089170.0235520993404-0.1121729466750.65620516567528.222924906153.469621882292.8173755019
41.874171695920.468737940743-0.1827801426361.14179380788-1.472340783138.983723020370.05722883981220.669322816520.17615303661-0.8822318508470.1541241438280.375991476231-0.970557981471-0.358344735194-0.215276585980.549535937238-0.0544594036942-0.0150744270720.425591834129-0.002661741943890.42753988675817.662917101938.544814125591.2615713325
54.57735924205-0.833357293704-0.5932249983763.54593242128-0.3380575891235.198885302940.00610921520052-0.3603944739690.1556614166951.11697694686-0.06138660933480.207594416913-0.176910944466-0.0938775055889-0.04420249711640.618292404384-0.0788379770977-0.000681251449620.2980811601-0.02992520163830.37325001770820.184860745937.8891897431107.391483774
62.451135191690.941525633785-0.3126932146732.2177797840.4563253091093.3136238447-0.141684228470.0592503628351-0.217102859391-0.3170790859790.122042755171-0.412187156508-0.2552891789920.3698720223390.01866456773710.332712761961-0.0684536441428-0.009015304321990.270637684184-0.02843059192480.3589480551721.479172062630.913384544296.2389172304
78.6072237885-2.413217379110.8357755368421.90693550762.029131743757.29948807691-0.261111110864-0.904891839157-0.0261265418191.99332550761-0.3356068414631.082612456650.540368449326-0.3617353536530.4985342948350.945318809992-0.1618253962110.1607812883420.477217427247-0.01924099039530.44387930070512.399368278431.432580064111.084443832
84.50820533432-1.123584211730.1862774288158.93936521335-1.86649839064.78472028677-0.390286565737-0.1579391445620.211495615874-0.6965570902650.364532138917-0.5378026982180.3522981512850.1452089338050.1041887862330.367237264231-0.121397837249-0.007871495028570.639617697323-0.03789319603670.34143448921221.8407765117.373988927466.0597293935
95.95777370003-0.166226250251-0.3872242253824.514481310310.4302366216236.49484601533-0.0136730288525-0.6867432953850.9080284935450.308199346089-0.4011501846430.406717454486-0.42844070921-0.1202323294450.379192419810.270437046348-0.017748360236-0.06030863826750.509100811777-0.1356590141640.44960934445310.58701858523.544508429264.1164374611
106.81601470529-1.84722354783-2.333214844963.146183207110.8746497954945.426351538130.2664910653340.775186896228-0.092810653159-0.62028187852-0.4756596412090.255022397601-1.09664951718-0.08956212509780.2743792465190.637256896890.00548704699129-0.09806509912830.368505506701-0.01123943136990.37095160898520.98678027831.197623698973.2013870376
113.50242692861-0.352633258096-0.09560943215212.4613908530.5226920283273.544702099620.1197742165910.2520218056640.225320032663-0.1284919098510.0731087112611-0.493383995673-0.7827616014890.64028374353-0.2045215260250.411205664072-0.1225839736950.03923933165230.397763265035-0.01591714316970.32536336919926.176819880729.114249705877.8435374619
121.6749290117-0.852645583653-0.4342615961248.6333002114-4.776086162946.985241798350.148825777174-0.305198395019-1.08761901452-0.278810170349-0.004648074087990.205334632810.724064311549-0.844670159653-0.1325697503470.43122625376-0.2773266688610.05328814689130.64517136431-0.02886789576610.6000786656020.89939760555514.1360238197102.445888438
138.269246274620.6274917504650.9585588137366.219468183260.9865422600784.879355870530.0927799526829-0.0157740210490.0716856816222-0.767010680636-0.08178839480130.791276481867-0.540696730696-0.688277198964-0.02685493625990.449784549436-0.0729796912678-0.04677489224960.635448612048-0.0612304732770.531218539272-1.1575206824326.4605888812100.874423213
147.51479900044-1.46845075673.853315235783.5915039493-0.2307323955422.077525419610.133612081720.07827089577-0.09817713493480.251418586153-0.3049730542970.646606025751-0.135054687196-1.113481658290.01448258135730.328815597712-0.1068896929710.03022577426241.10525199484-0.06628380323730.61657876521-8.016349489422.4078316353105.349220683
155.97255669937-0.8951538538321.048815885077.20425137397-1.270508272727.89568478081-0.3573072871540.45527057141-0.3363587742730.3035417745050.1626151233950.872319519211-0.55288563827-1.034687359040.0124947337460.411789025866-0.0440430301793-0.01523058702310.7436115117260.005948033820340.4211772239982.3349703396120.39264073190.2633778038
162.17213302346-0.469621533363-1.183811588011.90763445755-0.007576879468933.66751436362-0.2778134812310.50053754397-0.456549633142-0.0482917117018-0.08859430439030.277210196690.725020186852-0.4442481229270.2991906037320.382341857495-0.1842462318250.04741505397340.484902800056-0.06261621640940.4828430915948.3964903294714.741384090388.094113529
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 18 )AA2 - 181 - 17
22chain 'A' and (resid 19 through 37 )AA19 - 3718 - 36
33chain 'A' and (resid 38 through 57)AA38 - 5737 - 56
44chain 'B' and (resid 3 through 17 )BB3 - 171 - 15
55chain 'B' and (resid 18 through 29 )BB18 - 2916 - 27
66chain 'B' and (resid 30 through 47 )BB30 - 4728 - 45
77chain 'B' and (resid 48 through 58 )BB48 - 5846 - 56
88chain 'C' and (resid 1 through 18 )CC1 - 181 - 18
99chain 'C' and (resid 19 through 57 )CC19 - 5719 - 57
1010chain 'D' and (resid 5 through 24 )DD5 - 241 - 20
1111chain 'D' and (resid 25 through 57 )DD25 - 5721 - 53
1212chain 'E' and (resid 4 through 18 )EE4 - 181 - 15
1313chain 'E' and (resid 19 through 37 )EE19 - 3716 - 34
1414chain 'E' and (resid 38 through 57 )EE38 - 5735 - 54
1515chain 'F' and (resid 3 through 24 )FF3 - 241 - 22
1616chain 'F' and (resid 25 through 56 )FF25 - 5623 - 54

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