[English] 日本語
Yorodumi
- PDB-8arc: Heterologous Complex of Aeromonas hydrophila Type III secretion s... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8arc
TitleHeterologous Complex of Aeromonas hydrophila Type III secretion substrate AscX with Photorhabdus luminescens subsp. laumondii LscY
Components
  • AscX
  • Type III secretion protein SctY
KeywordsCHAPERONE / Type III Secretion System / T3SS / SctX / SctY
Function / homology
Function and homology information


Tetratricopeptide repeat / Type III secretion system YscX / Type III secretion system chaperone, YscY / Type III secretion system YscX (type_III_YscX) / Tetratricopeptide repeat domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha
Similarity search - Domain/homology
BROMIDE ION / AscX / Type III secretion protein SctY
Similarity search - Component
Biological speciesPhotorhabdus laumondii subsp. laumondii TTO1 (bacteria)
Aeromonas hydrophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsGilzer, D. / Niemann, H.H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2023
Title: The type III secretion chaperone SctY may shield the hydrophobic export gate-binding C-terminus of its substrate SctX.
Authors: Gilzer, D. / Kowal, J.L. / Flottmann, F. / Niemann, H.H.
History
DepositionAug 16, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 26, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 21, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _pdbx_initial_refinement_model.accession_code

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Type III secretion protein SctY
B: AscX
C: Type III secretion protein SctY
D: AscX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,49810
Polymers44,0194
Non-polymers4796
Water32418
1
A: Type III secretion protein SctY
B: AscX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3296
Polymers22,0092
Non-polymers3204
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Type III secretion protein SctY
D: AscX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1694
Polymers22,0092
Non-polymers1602
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.590, 34.220, 99.600
Angle α, β, γ (deg.)90.000, 101.810, 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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid -1 through 24 or resid 26...
d_2ens_1(chain "C" and (resid -1 through 24 or resid 26...
d_1ens_2chain "B"
d_2ens_2(chain "D" and (resid 50 through 63 or resid 67 through 118))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1HISPROA1 - 26
d_12ens_1ARGARGA28 - 47
d_13ens_1ALAALAA49 - 97
d_14ens_1SERGLNA99 - 107
d_15ens_1BRBRB
d_21ens_1HISPROI1 - 26
d_22ens_1ARGARGI28 - 47
d_23ens_1ALAALAI49 - 97
d_24ens_1SERGLNI99 - 107
d_25ens_1BRBRJ
d_11ens_2ARGLEUG1 - 66
d_21ens_2ARGHISM1 - 14
d_22ens_2HISLEUM18 - 69

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.999929644166, -0.00626301040684, 0.0100737985856), (-0.00560855760386, 0.997951332379, 0.0637313289159), (-0.0104523106969, 0.0636703455655, -0.997916247135)34.2998444205, -1.28694988494, 49.0358378378
2given(-0.999998450175, 0.0017082590537, -0.000426026894616), (0.00167329071122, 0.997421463643, 0.0717469439197), (0.000547490735306, 0.0717461198577, -0.997422776228)34.7873288303, -1.78839994306, 48.8706321183

-
Components

#1: Protein Type III secretion protein SctY


Mass: 13401.528 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photorhabdus laumondii subsp. laumondii TTO1 (bacteria)
Gene: sctY, plu3762 / Plasmid: pACYCDuet-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q7N0W7
#2: Protein AscX


Mass: 8607.969 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: N-terminal residues GAM remain after TEV-cleavage of the N-terminal MBP-tag.
Source: (gene. exp.) Aeromonas hydrophila (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q699R5
#3: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Br
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 1.73 Å3/Da / Density % sol: 29 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: reservoir solution: 0.15 M KBr, 24-26%(w/v) PEG2000 monomethyl ester; protein: 5 mg/mL in 20 mM Tris pH 8, 150 mM NaCl, 2 mM TCEP; drop size: 0.66 uL protein + 0.33 uL reservoir

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9187 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 2, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9187 Å / Relative weight: 1
ReflectionResolution: 2.1→48.8 Å / Num. obs: 32409 / % possible obs: 94.8 % / Redundancy: 1.99 % / Biso Wilson estimate: 44.94 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.063 / Net I/σ(I): 8.64
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 2 % / Mean I/σ(I) obs: 1.23 / Num. unique obs: 2393 / CC1/2: 0.588 / Rrim(I) all: 1.295 / % possible all: 94.7

-
Processing

Software
NameVersionClassification
XDS20210205data reduction
XSCALE20220220data scaling
PHASER2.8.3phasing
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7QIH

7qih


Resolution: 2.1→48.75 Å / SU ML: 0.2865 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.7251
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2862 1582 4.9 %
Rwork0.2286 30694 -
obs0.2313 32276 94.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 67.91 Å2
Refinement stepCycle: LAST / Resolution: 2.1→48.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2776 0 6 18 2800
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00152853
X-RAY DIFFRACTIONf_angle_d0.4373851
X-RAY DIFFRACTIONf_chiral_restr0.029428
X-RAY DIFFRACTIONf_plane_restr0.0025498
X-RAY DIFFRACTIONf_dihedral_angle_d11.86571092
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.80765896232
ens_2d_2BX-RAY DIFFRACTIONTorsion NCS0.825954507966
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.170.42461380.35882768X-RAY DIFFRACTION93.83
2.17-2.250.3731570.32592804X-RAY DIFFRACTION95.64
2.25-2.340.31331460.31642836X-RAY DIFFRACTION95.98
2.34-2.440.38151550.29122895X-RAY DIFFRACTION95.97
2.44-2.570.27821450.26842771X-RAY DIFFRACTION95.42
2.57-2.730.2811390.2722836X-RAY DIFFRACTION96.22
2.73-2.940.28891450.25252842X-RAY DIFFRACTION96.64
2.94-3.240.32091480.24842858X-RAY DIFFRACTION95.43
3.24-3.710.27061370.22112722X-RAY DIFFRACTION92.29
3.71-4.670.24621380.18992649X-RAY DIFFRACTION90.49
4.67-48.750.26491340.18522713X-RAY DIFFRACTION90.76
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)
17.179440761542.658904246893.760121043170.9847311068861.392226310231.9693451824-0.18401492611-0.820423552919-1.10380047091.40530598849-0.2092739819340.05046878885960.916789277607-0.101897292474-0.7118609100860.8123953096740.213733627070.2258438297630.4778173487190.14625043570.52702189955825.3964732201-14.081673425822.4119138718
29.483928795113.10032907823-3.65373429653.98541246481-1.25091365469.9764550659-0.723399719012-1.76274143122-0.8641454532770.398591654517-0.198360534829-0.2087559256891.877492305790.2066410857371.575098446410.6796671705560.07748114435560.1919851904431.10849952487-0.04480312072970.39767225372537.3249781919-7.091462743817.49618696348
30.7642045846970.746190730967-0.4762089235141.104045086980.4518151204232.52414924462-0.308389543727-0.0700307866953-0.311833462216-0.031802077340.03958857352710.08206883715240.321039949247-0.892250703495-0.1665985234870.4351456381450.03910471898090.08779547508680.5423269274860.02456755335790.1853642106047.5060128524-5.5124711764731.7837020145
43.989614177941.715273775650.9635119819383.489458428280.4201444251656.95144618849-0.479717787558-0.1924769504090.261098247445-0.5323494172580.0835051140335-0.0818009872958-0.5547093462190.2616937103540.4200523516240.4680086927130.03903408996580.002403649621590.350760901661-0.01833133127570.20267280289317.70162353633.4573094237733.2474153029
53.147797277091.997776077021.646139078918.737770891430.277596809366.76954869986-0.250047936826-0.048875819520.134903574649-1.01563495751-0.0206132901313-0.887384658877-0.1228583258161.26766745381-0.1191839667520.5074566548590.04749814975960.01363233530970.780470464824-0.06708650445270.31102324040826.51481368088.896908610843.0065369944
67.5777353748-0.9491920636125.741707876916.19289065498-5.396876673767.95131022662-0.406078082034-1.84267162544-0.584535380310.943422502748-0.5214362435850.5708581206961.05468271258-1.314774482281.173879565790.8611133223690.01133760679410.1002012125190.994640538216-0.09937693910830.39328605043415.05595006842.126932766947.6491164088
77.67978810594-2.47053739370.826824080430.84899720087-0.1441005597870.7432095062520.264469328804-0.7766428814590.8819637539630.419215323898-0.113851059796-0.01523314547430.542804771898-0.40018727066-0.4501975986850.8284459116530.1299377693880.2550142603320.794004968746-0.04561760285140.399358547626-1.791958760272.8774015112436.847552747
89.53029935065-2.72543109228-6.407239857767.61828188701-0.8536110993488.18782761678-0.2798067760330.759538404486-1.16935007946-0.441557665091-0.1034346843950.3007392204811.11665322318-1.233520492490.3688532021620.883633159039-0.2200420108950.04726158375820.838325008085-0.02073858491880.5798418188512.28396624573-11.13733196826.7166896099
96.483541160180.624975325585-2.587494122632.43932400109-1.894436510017.34351241807-0.8920599795031.29815669596-0.350473233067-0.6994275141550.118949841078-0.09350884470731.335568236890.1284987147533.4253707970.624712071145-0.1930685478320.1144923203091.151920136830.2070571964510.419137502492-3.02777877833-7.7666077447241.0278604943
101.16950324280.181191963616-2.506038628343.31146174816-0.4605003010815.38286295674-0.2040248044090.484106797062-0.3299086346240.3026547715310.222503260079-0.153440950470.8470942779071.233699233190.3487931165550.436919647570.02583861090860.09709247107380.56011344649-0.02124195535960.25883956054927.3661711787-4.640264188616.9548193203
113.14849937722-1.245601299811.043113245690.67128606211-1.009318068956.11944227139-0.3808174588750.1485059998460.283724988980.2493914453670.1068164643950.0350348630108-0.809141231429-0.361229434253-0.1286238559920.472673223446-0.01925063301690.03097535550460.4517802013050.110772542650.15928051643616.89789539754.2040825578516.0774581498
124.19986172643-1.00620725989-1.14337656168.21506608854-4.165609968054.70705910393-0.214844431058-0.7889770419380.05476464741251.325679405370.2403436545340.756467512326-0.748802456854-1.73684098751-0.122694103190.7682446705980.078366424950.05902498994980.9874707426240.06153338986860.4196362673058.377438232099.991251896656.38533598206
130.767225766015-0.3478914922151.143374686478.16818042367.44210629369.61282437704-0.1633102552860.782473147262-0.103961978146-0.771712648118-0.37776741196-1.527697510890.3729743600820.5568550218722.876274698170.925269536128-0.1135100505490.1217662824311.188362534550.3256394863130.59742430210619.79895885183.965439624151.61851293588
147.343368673843.751437941096.977940104813.099553283723.485964410646.63589826578-1.32911594360.8230724336072.01559809156-0.4607562805440.2418420583050.0403378463871.311075860492.880698963830.9479928159550.899366895016-0.0625887624534-0.03312192871441.321256494780.2225899855260.68388448729130.7178566276.5098129511211.5701278313
156.936198990891.963001772374.710387889215.865287555063.348765446325.16269621830.467843739620.9011763034972.21517897063-0.04703844860060.141754665120.4297484498210.4127502198921.59296373231-0.09511438935170.958223609421-0.3664571988380.2948618543411.332313570750.05569145974230.80036686506642.16695774062.6120032931713.8845094441
167.002904634293.18174724064-3.805765719197.45646405802-0.0707956411217.50321631229-0.255565684063-1.53380769271-1.151374225310.3165460098010.358189662189-1.28361787048-1.691714319641.62315798150.08625730907020.8642563801420.1312657582310.1567780048791.05104748515-0.08722653981510.69528854845838.301134152-8.2157918938521.1452449119
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'D' and (resid 89 through 103 )DM89 - 10340 - 54
22chain 'D' and (resid 104 through 118 )DM104 - 11855 - 69
33chain 'A' and (resid -1 through 37 )AA-1 - 371 - 39
44chain 'A' and (resid 38 through 75 )AA38 - 7540 - 77
55chain 'A' and (resid 76 through 105 )AA76 - 10578 - 107
66chain 'B' and (resid 50 through 59 )BG50 - 591 - 10
77chain 'B' and (resid 60 through 71 )BG60 - 7111 - 19
88chain 'B' and (resid 72 through 104 )BG72 - 10420 - 52
99chain 'B' and (resid 105 through 118 )BG105 - 11853 - 66
1010chain 'C' and (resid -1 through 37 )CI-1 - 371 - 39
1111chain 'C' and (resid 38 through 75 )CI38 - 7540 - 77
1212chain 'C' and (resid 76 through 105 )CI76 - 10578 - 107
1313chain 'D' and (resid 50 through 59 )DM50 - 591 - 10
1414chain 'D' and (resid 60 through 66 )DM60 - 6611 - 17
1515chain 'D' and (resid 67 through 71 )DM67 - 7118 - 22
1616chain 'D' and (resid 72 through 88 )DM72 - 8823 - 39

+
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://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