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- PDB-8daa: Coevolved affibody-Z domain pair LL2.c7 -

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Basic information

Entry
Database: PDB / ID: 8daa
TitleCoevolved affibody-Z domain pair LL2.c7
Components
  • Affibody LL2.FIVK
  • 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
MALONATE ION / Immunoglobulin G-binding protein A
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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 LL2.FIVK
C: Immunoglobulin G-binding protein A
D: Affibody LL2.FIVK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8905
Polymers30,7884
Non-polymers1021
Water59433
1
A: Immunoglobulin G-binding protein A
B: Affibody LL2.FIVK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4963
Polymers15,3942
Non-polymers1021
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-6 kcal/mol
Surface area6310 Å2
MethodPISA
2
C: Immunoglobulin G-binding protein A
D: Affibody LL2.FIVK


Theoretical massNumber of molelcules
Total (without water)15,3942
Polymers15,3942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-7 kcal/mol
Surface area6550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.588, 53.023, 68.662
Angle α, β, γ (deg.)90.000, 98.390, 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
Components on special symmetry positions
IDModelComponents
11D-109-

HOH

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Components

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


Mass: 7761.548 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
#2: Protein Affibody LL2.FIVK


Mass: 7632.561 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: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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

Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 3.0 M Ammonium sulfate, 100 mM HEPES pH 7.0 cryoprotected with sodium malonate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 8, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.75→23.48 Å / Num. obs: 17068 / % possible obs: 95.16 % / Redundancy: 3.8 % / Biso Wilson estimate: 30.47 Å2 / CC1/2: 0.991 / CC star: 0.998 / Rmerge(I) obs: 0.2109 / Rpim(I) all: 0.1212 / Rrim(I) all: 0.2443 / Net I/σ(I): 6.49
Reflection shellResolution: 1.75→1.813 Å / Redundancy: 3.8 % / Rmerge(I) obs: 1.973 / Mean I/σ(I) obs: 0.61 / Num. unique obs: 1711 / CC1/2: 0.356 / CC star: 0.725 / Rpim(I) all: 1.158 / Rrim(I) all: 2.297 / % possible all: 95.52

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Processing

Software
NameVersionClassification
Blu-Ice1data collection
PHENIX1.20.1_4487refinement
BUSTERrefinement
XDSdata reduction
PHASERphasing
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5djt

5djt


Resolution: 1.75→23.48 Å / SU ML: 0.3819 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 37.8798
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2985 1705 10.01 %random selection
Rwork0.2509 15321 --
obs0.2558 17026 95.22 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36 Å2
Refinement stepCycle: LAST / Resolution: 1.75→23.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1712 0 7 33 1752
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00211745
X-RAY DIFFRACTIONf_angle_d0.45992376
X-RAY DIFFRACTIONf_chiral_restr0.0347270
X-RAY DIFFRACTIONf_plane_restr0.0032327
X-RAY DIFFRACTIONf_dihedral_angle_d14.038630
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.80.42771420.42481279X-RAY DIFFRACTION95.75
1.8-1.860.42641390.4111253X-RAY DIFFRACTION94.18
1.86-1.930.40241390.36881243X-RAY DIFFRACTION93.13
1.93-20.3831410.35251265X-RAY DIFFRACTION96.1
2-2.090.38881410.33121263X-RAY DIFFRACTION95.77
2.09-2.20.35411450.28371297X-RAY DIFFRACTION95.81
2.2-2.340.34151420.25121276X-RAY DIFFRACTION95.88
2.34-2.520.29481370.23831244X-RAY DIFFRACTION93.18
2.52-2.780.28911500.24531340X-RAY DIFFRACTION97.96
2.78-3.180.29961420.23581282X-RAY DIFFRACTION97.2
3.18-40.25631420.21561276X-RAY DIFFRACTION93.66
4-23.480.25321450.21561303X-RAY DIFFRACTION94.27
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)
14.742113208162.51662944013-1.242340105821.4839337175-0.3207441201592.056043206180.168646521480.1195189147160.08671170976880.0944933053859-0.129326770871-0.5311411712920.123419831482-0.306520682185-0.1318207839160.224224340138-0.0351869672119-0.01151350681530.260814328592-0.03176054077380.254344306716-16.4082894805-5.3811811533939.6074838227
21.196675277221.834253354740.5937780737638.16839448040.9380474796663.15883024396-0.021269733840.143320779069-0.2315342201450.6239000643720.147770563637-0.4132840829690.2137316211070.115549463515-0.1436267729540.293910014439-0.00184973009541-0.04040715592980.218260369158-0.01512162064570.295643850438-18.5481331154-12.600892330242.2142728331
30.0772070892772-0.01170240203730.02977756984540.083221805334-0.01835920635120.01872778185880.469338619158-0.03654212020290.404393815191-1.254895277410.596977017184-0.262072863435-0.1242431133360.642054097199-0.004756654767410.6722998988660.0845813770734-0.04560503090450.662908185903-0.1749979460471.10366896544-30.336871734-15.63118692724.0559499033
43.281518628883.039646606112.799424120323.145754300841.965431413763.54101731670.819340014063-0.2620935804330.001097374477430.485204996263-0.5512197299980.5086525454920.411575197526-0.576724959462-0.001679697032120.4289323665360.007639749881190.02638706607490.271736835107-0.01009738058290.453571356784-14.902674341-9.5009115439228.8542397385
53.753079361923.01476159273-1.4662036122.27000067905-1.065887573653.666104875020.4819109978930.1885503005050.04367456844440.270234352144-0.1522288899850.119239667905-0.367401815631-0.393684194923-0.132721733290.2980570878260.0655305799435-0.01192119497910.205667071180.03858193289930.292210108877-13.85663111090.15374249791829.4670176104
62.569312414823.40099246615-0.5314964011944.49303703437-0.8801471401013.949027993970.2756075493860.5401489543070.606247232545-0.116515318636-0.07385421840730.356540481483-0.248110259382-0.46497835348-0.1075706782360.2094805026730.05437815442190.007727257898990.237303431431-0.0005446590871070.261133327392-11.3669910374-0.95627173804420.9728426925
70.0990875635176-0.0124322696353-0.0746854248740.1710696805940.028591552990.0525832763824-0.1986031175250.395197451590.0184200904941-0.02124926547610.6246747335630.306767810988-0.555627617131-0.100775865333-0.00077950057240.6864391164290.03941347767140.08832887422190.417210341798-0.06461299514910.66292808808828.3414726073.6058869671-9.27113358028
83.01131361918-1.23721221828-0.02935814519651.901991140710.6911228274171.143696692490.01619593664460.1246376567480.2801257414060.3660754113290.1113931931730.512619251759-0.0332156231479-0.09902448628440.03818053676530.3591035363040.013741911925-0.009475391686720.2218953243910.04039046853090.358508469579.7645590695-4.68985888858-4.71961124703
91.44583672048-1.73884312223-0.8116744816556.87251841060.1790525286994.59966844633-0.189546700910.0398821683606-0.23676716237-0.02210457401670.1767724990440.2878506164160.1812771471820.0064332855407-0.09080105998930.3099386511180.0131496269239-0.03331545597150.1788014562580.001837837738460.29343749179613.1968742557-10.9831746047-7.94730066964
102.86340725235-2.91130344132-1.374057692825.21245017924-3.482870076751.999625382310.2560054818690.239298967478-0.08846045206010.6146423096040.6235416508540.793084195487-0.498009942842-1.173408947370.3465267212380.5850755136160.0970248056662-0.1347941836410.316150698576-0.1516140679571.2637222781625.7005788455-14.37515658889.58325377877
112.95020916794-2.3779231208-0.9759720375242.59241962085-0.2556609046822.23292760074-0.1502681213990.304296978477-0.5275032679060.1191435352360.08380521227970.4031200480680.6825226992350.54881797492-0.1140563643080.3984302474280.0102990940502-0.03286475875620.2845581272140.005602771169510.35992410100710.5548400315-8.456608094575.27374552917
125.32316091542-1.61524473052-0.2781382493920.846354560789-0.5248626212723.131672864770.3147635039340.0454508294707-0.131827642198-0.185022775953-0.1242172127280.163219717192-0.3448008948720.0417723221122-0.05658700878190.266350570598-0.0283963970054-0.02967276990420.143812452176-0.02241820220020.3029730747818.943027287411.695725809784.54613620742
137.84813624534-2.16822635938-2.688618488752.61384476751.23339432442.213176093140.150376306149-0.9690890235910.05271598659780.1955401937720.10768960883-0.04920727868780.08720356825730.103084137162-0.062302376480.256345556301-0.049205767868-0.03245223939580.1996551358730.02892217294550.2524824832496.29624887520.48442571709513.0220658502
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 4 through 23 )AA4 - 231 - 20
22chain 'A' and (resid 24 through 56 )AA24 - 5621 - 53
33chain 'B' and (resid 0 through 4 )BC0 - 41 - 5
44chain 'B' and (resid 5 through 17 )BC5 - 176 - 18
55chain 'B' and (resid 18 through 37 )BC18 - 3719 - 38
66chain 'B' and (resid 38 through 57 )BC38 - 5739 - 58
77chain 'C' and (resid 0 through 5 )CD0 - 51 - 6
88chain 'C' and (resid 6 through 23 )CD6 - 237 - 24
99chain 'C' and (resid 24 through 57 )CD24 - 5725 - 58
1010chain 'D' and (resid 0 through 4 )DE0 - 41 - 5
1111chain 'D' and (resid 5 through 17 )DE5 - 176 - 18
1212chain 'D' and (resid 18 through 37 )DE18 - 3719 - 38
1313chain 'D' and (resid 38 through 57 )DE38 - 5739 - 58

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