[English] 日本語
Yorodumi
- PDB-8da4: Coevolved affibody-Z domain pair LL1.c2 -

+
Open data


ID or keywords:

Loading...

-
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
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: 1.92 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more