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- PDB-8da9: Coevolved affibody-Z domain pair LL2.c3 -

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Basic information

Entry
Database: PDB / ID: 8da9
TitleCoevolved affibody-Z domain pair LL2.c3
Components
  • (Affibody LL2. ...) x 2
  • Immunoglobulin G-binding protein A
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: 1.35 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
B: Affibody LL2.FIIV
C: Immunoglobulin G-binding protein A
D: Affibody LL2.FIIV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4189
Polymers30,9454
Non-polymers4725
Water2,414134
1
A: Immunoglobulin G-binding protein A
B: Affibody LL2.FIIV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6474
Polymers15,4592
Non-polymers1882
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-23 kcal/mol
Surface area7030 Å2
MethodPISA
2
C: Immunoglobulin G-binding protein A
D: Affibody LL2.FIIV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7705
Polymers15,4862
Non-polymers2843
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2030 Å2
ΔGint-32 kcal/mol
Surface area7060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.403, 54.259, 68.601
Angle α, β, γ (deg.)90.000, 94.410, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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Affibody LL2. ... , 2 types, 2 molecules BD

#2: Protein Affibody LL2.FIIV


Mass: 7643.585 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 LL2.FIIV


Mass: 7670.631 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 , 1 types, 2 molecules AC

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


Mass: 7815.640 Da / Num. of mol.: 2 / Mutation: Q9L, F13V, 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 , 3 types, 139 molecules

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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 1.6 Å3/Da / Density % sol: 23.18 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.4 M Ammonium sulfate 0.1M HEPES pH 7.0 Cryoprotected with 30% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.88557 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 16, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.88557 Å / Relative weight: 1
ReflectionResolution: 1.35→38 Å / Num. obs: 41323 / % possible obs: 95.84 % / Redundancy: 6.8 % / Biso Wilson estimate: 17.62 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.1129 / Rpim(I) all: 0.0467 / Rrim(I) all: 0.1224 / Net I/σ(I): 8.93
Reflection shellResolution: 1.35→1.398 Å / Redundancy: 93.56 % / Rmerge(I) obs: 3.679 / Mean I/σ(I) obs: 0.76 / Num. unique obs: 4054 / CC1/2: 0.172 / CC star: 0.542 / Rpim(I) all: 1.522 / Rrim(I) all: 3.989 / % possible all: 93.56

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Processing

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

5djt


Resolution: 1.35→38 Å / SU ML: 0.1875 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.4308
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.1981 1640 3.98 %random selection
Rwork0.1754 39553 --
obs0.1763 41193 95.85 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.47 Å2
Refinement stepCycle: LAST / Resolution: 1.35→38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1820 0 27 134 1981
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141892
X-RAY DIFFRACTIONf_angle_d1.31352572
X-RAY DIFFRACTIONf_chiral_restr0.0762281
X-RAY DIFFRACTIONf_plane_restr0.0095345
X-RAY DIFFRACTIONf_dihedral_angle_d13.2621712
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.390.40911390.36393202X-RAY DIFFRACTION93.8
1.39-1.430.36561240.35183101X-RAY DIFFRACTION90.56
1.43-1.490.27921360.26093293X-RAY DIFFRACTION96.16
1.49-1.550.251280.23723287X-RAY DIFFRACTION96.41
1.55-1.620.22551460.21433305X-RAY DIFFRACTION96.56
1.62-1.70.22661290.19243334X-RAY DIFFRACTION96.89
1.7-1.810.22911370.18963252X-RAY DIFFRACTION94.19
1.81-1.950.20491350.16443330X-RAY DIFFRACTION97.44
1.95-2.140.17381480.15363360X-RAY DIFFRACTION98.07
2.14-2.450.1761470.14343348X-RAY DIFFRACTION97.25
2.45-3.090.18881300.16193345X-RAY DIFFRACTION96.34
3.09-380.17711410.16393396X-RAY DIFFRACTION96.51
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)
13.59809936512-3.358669523960.5716462000913.06718504655-0.5079808967170.121407346789-0.0235503530527-0.06063462426140.397540914904-0.239864621480.08843650076910.114980492025-0.17626164981-0.0947300642769-0.02718847294710.2681315790590.04011315424390.005495216562020.241430803178-0.001549312264650.27915815740326.407410123155.10734038467.97391729337
27.73341484227-4.10357705036-4.624205471239.244914104351.438206657418.457287930760.3612464517880.1338911165670.199280628004-0.346123006388-0.237924350802-0.33891486076-0.3643603784750.114998526202-0.1247331771830.1780112877270.005170549934560.007158795005340.1329928009540.007510771547390.11652464822640.836479577648.78530442153.82140979177
39.47259928632-0.1436962640311.22122925533.93589014702-0.1527611539231.90461754641-0.03327498238780.173650104113-0.168396642433-0.2757496239250.0942700611028-0.01482531488320.1123971056640.0801447725185-0.0291462311590.180534411874-0.01211010738660.003992436136970.139050873276-0.002586714144210.098360867285838.584155938539.04832442783.64457313392
43.53560119266-5.39418811032-0.5343935348858.733087891960.3911007257363.024982105040.0130325276268-0.4673088644280.07293688787760.0161907928790.149742154255-0.3018165474450.02831981313910.143976562519-0.1378158815950.13003870433-0.00808772159916-0.01764598689660.147535436501-0.0149960401170.1265387346941.979135305841.51513802611.9956798504
54.326922326854.97364348547-1.654276596695.71728080654-1.371296164933.405387941010.0743892895841-0.246112044603-0.904428504692-0.1672410940050.240055751611-0.209178008492-0.04701149310030.0319069804754-0.1833487055490.267559182228-0.04383356961010.004293993983820.252037115946-0.003565426216040.37698721162529.525471018737.9713145019-8.21768209167
64.323562899132.68937863419-1.386980734263.29667019129-0.08179156866731.66789059410.0432679996151-0.0233658803538-0.1774425129870.169612031117-0.054358877661-0.2638663945170.01661278471760.04905445306360.006910044130440.169618169328-0.00153403640942-0.01190024645920.1412534441730.01742692440870.12921009959443.146834945550.4171133209-4.84789715481
73.035064203934.28997868367-0.1771159675796.14892545278-0.05256006132033.4522566352-0.1087053986730.35401874328-0.14547050796-0.2032857814040.141164513165-0.375882099468-0.1714584429380.277225875715-0.01476524602850.158739353298-0.03024290750310.005928354494970.134884889503-0.004079646656760.15192999834645.209475824151.9822951487-13.4641530257
83.772362556143.36573594583-1.900804278212.97923303134-1.748385528110.9713297066850.0195252894655-0.1516593563110.547964563294-0.0746937735420.0709565495272-0.0126173430539-0.07686968788350.154534410454-0.1986153949940.216401659275-0.0137067022680.00820379629720.217683602896-0.02565972323050.23017675044222.380676837251.822187286226.6713383949
94.922363326550.5205663275730.6883126879485.324963627370.4248057384032.574593482140.0510256585296-0.0246670206647-0.02238448338750.149368246427-0.08104003553530.151662882162-0.00722983983713-0.1404648375650.03463200573390.132379353028-0.003931792864110.01279884452560.120570328538-0.009951682337270.086581559132410.965745513439.063636241230.5578276898
104.070467100466.09606440478-0.1926238143029.24496587718-0.2558604250542.47747333391-0.05679713729470.4003301866380.105664470859-0.2023157787350.1498759064650.2825796895770.0085424930148-0.150365114321-0.03109018553850.1331754901460.00437532596134-0.01312755322880.1473456630760.005556169772860.1192278682619.8203160615339.182754352121.8376942267
111.081953829090.844086358265-1.164537010754.35115934370.3394622878342.085767315210.39354045804-0.225691803166-0.7922337350330.02982413734730.149797455384-0.1247169079110.3741515451330.292536756055-0.3624733425740.2548882070080.0620475430591-0.05102442764030.232697457571-0.05509342702280.31120545716319.048396989936.605690953641.2668561641
126.63721813527-5.038521172422.996017543863.96937490996-1.435802739027.107449696040.343339191757-0.377414009635-0.496508901228-0.141058847994-0.0274119403940.5167816883810.355801814278-0.114345104439-0.2290525867030.179378015483-0.0137197005517-0.02625149803580.1842132268480.003268065457310.2546194447764.3109878854942.833307128638.8886229344
133.52399046749-0.901614894672-0.8096951123542.37776157379-0.02156386833282.423073061640.09398886714460.0463597358830.004620203025940.0101834656496-0.07529387638820.114150355617-0.081882297569-0.0896550113329-0.02310053625790.1314690869220.003033921418730.005023762429460.118189733626-0.01459980213540.1095558685477.5232929422651.517981138738.3423803554
146.07896644031-4.739808163470.7527699368735.49581774365-0.8300710806982.26404943365-0.163261924449-0.573265478590.03531409528580.1001872510360.194234637801-0.090548008590.0170320679784-0.0883251768048-0.0783677704550.1301491104570.03426564927720.009947856436990.1491108061870.004929697034930.1053164420944.3179522650550.011635796446.9682259526
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 0 through 8 )AA0 - 81 - 9
22chain 'A' and (resid 9 through 18 )AA9 - 1810 - 19
33chain 'A' and (resid 19 through 37 )AA19 - 3720 - 38
44chain 'A' and (resid 38 through 57 )AA38 - 5739 - 58
55chain 'B' and (resid 0 through 8 )BB0 - 81 - 9
66chain 'B' and (resid 9 through 37 )BB9 - 3710 - 38
77chain 'B' and (resid 38 through 57 )BB38 - 5739 - 58
88chain 'C' and (resid 0 through 11 )CD0 - 111 - 12
99chain 'C' and (resid 12 through 37 )CD12 - 3713 - 38
1010chain 'C' and (resid 38 through 57 )CD38 - 5739 - 58
1111chain 'D' and (resid 0 through 9 )DE0 - 91 - 10
1212chain 'D' and (resid 10 through 18 )DE10 - 1811 - 19
1313chain 'D' and (resid 19 through 37 )DE19 - 3720 - 38
1414chain 'D' and (resid 38 through 57 )DE38 - 5739 - 58

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