[English] 日本語
Yorodumi
- PDB-7qih: Complex of the Yersinia enterocolitica Type III secretion protein... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7qih
TitleComplex of the Yersinia enterocolitica Type III secretion proteins YscX and YscY
Components
  • Chaperone protein YscY
  • Yop proteins translocation protein X
KeywordsCHAPERONE / Type III Secretion System / T3SS / SctX / SctY
Function / homologyType III secretion system YscX / Type III secretion system chaperone, YscY / Type III secretion system YscX (type_III_YscX) / Tetratricopeptide-like helical domain superfamily / extracellular region / cytoplasm / Chaperone protein YscY / Yop proteins translocation protein X
Function and homology information
Biological speciesYersinia enterocolitica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsGilzer, D. / Niemann, H.H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2022
Title: Direct interaction of a chaperone-bound type III secretion substrate with the export gate.
Authors: Gilzer, D. / Schreiner, M. / Niemann, H.H.
History
DepositionDec 15, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 1, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Chaperone protein YscY
B: Yop proteins translocation protein X
C: Chaperone protein YscY
D: Yop proteins translocation protein X


Theoretical massNumber of molelcules
Total (without water)45,4634
Polymers45,4634
Non-polymers00
Water1,22568
1
A: Chaperone protein YscY
B: Yop proteins translocation protein X


Theoretical massNumber of molelcules
Total (without water)22,7322
Polymers22,7322
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Chaperone protein YscY
D: Yop proteins translocation protein X


Theoretical massNumber of molelcules
Total (without water)22,7322
Polymers22,7322
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.553, 140.833, 59.880
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

-
Components

#1: Protein Chaperone protein YscY / / Yop proteins translocation protein Y


Mass: 14077.914 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: YscY with N-terminal hexahistidine tag / Source: (gene. exp.) Yersinia enterocolitica (bacteria) / Gene: yscY / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0C2N2
#2: Protein Yop proteins translocation protein X


Mass: 8653.756 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: N-terminally truncated YscX / Source: (gene. exp.) Yersinia enterocolitica (bacteria) / Gene: yscX / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0C2N4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 68 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.93 Å3/Da / Density % sol: 36.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: Protein Concentration: 3-5 mg/mL; Protein Buffer: 20 mM Tris pH 8.0, 150 mM NaCl, 5 mM TCEP; Reservoir Solution: 0.1 M BisTris pH 6.0, 0.2 M MgCl2, 13-21 % PEG 3350; Drop Ratio: 0.33 uL ...Details: Protein Concentration: 3-5 mg/mL; Protein Buffer: 20 mM Tris pH 8.0, 150 mM NaCl, 5 mM TCEP; Reservoir Solution: 0.1 M BisTris pH 6.0, 0.2 M MgCl2, 13-21 % PEG 3350; Drop Ratio: 0.33 uL Reservoir + 0.66 uL Protein
PH range: 5.5-6.2

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.92→45.62 Å / Num. obs: 27713 / % possible obs: 99.7 % / Redundancy: 12.78 % / Biso Wilson estimate: 39.5 Å2 / CC1/2: 1 / Rrim(I) all: 0.102 / Net I/σ(I): 16.4
Reflection shellResolution: 1.92→2.03 Å / Redundancy: 11.29 % / Mean I/σ(I) obs: 0.78 / Num. unique obs: 4312 / CC1/2: 0.446 / Rrim(I) all: 2.941 / % possible all: 98

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
PHASERphasing
BUCCANEERmodel building
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold2 model

Resolution: 1.92→45.62 Å / SU ML: 0.3125 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.4098
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2624 1382 5 %
Rwork0.2206 26232 -
obs0.2226 27614 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.27 Å2
Refinement stepCycle: LAST / Resolution: 1.92→45.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2883 0 0 68 2951
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00162960
X-RAY DIFFRACTIONf_angle_d0.38944011
X-RAY DIFFRACTIONf_chiral_restr0.0274448
X-RAY DIFFRACTIONf_plane_restr0.002526
X-RAY DIFFRACTIONf_dihedral_angle_d12.49431106
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.92-1.990.48541320.47072491X-RAY DIFFRACTION96.22
1.99-2.070.37941350.35212578X-RAY DIFFRACTION99.85
2.07-2.160.3511360.30042581X-RAY DIFFRACTION99.89
2.16-2.270.30841370.26752597X-RAY DIFFRACTION99.78
2.27-2.420.26711380.23062609X-RAY DIFFRACTION99.93
2.42-2.60.27471390.23282635X-RAY DIFFRACTION99.86
2.6-2.860.30541370.23362601X-RAY DIFFRACTION99.96
2.87-3.280.25331380.24042649X-RAY DIFFRACTION99.75
3.28-4.130.24251420.1922685X-RAY DIFFRACTION99.96
4.13-45.620.21851480.18242806X-RAY DIFFRACTION99.29
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)
18.567562389461.984665544164.145764149428.219722450410.3559886685898.82749926383-0.109301768390.08073915584070.512542605660.0881071805557-0.02650764712940.520617323060.04852996692920.07650708697970.09228806550680.2854391504610.02347268811180.0488252908520.2591557215330.03091515850920.213373971578-29.417796461518.8486325464-23.0041878663
24.626968672911.20630496874-1.037008948387.420174067662.040095920055.38776928125-0.446412232776-0.493902502856-1.41569135646-0.04182057658760.690963610357-0.3645994140040.2567038370680.283293485062-0.1813711612260.4050212527660.06142066912050.09116891343190.2626902114280.01003775494770.341276075362-22.359813430313.5638606302-26.0276941279
37.972993891020.5804156371073.812503147883.02970631997-2.373926891798.602717353130.1096680969580.199602115592-0.309368326416-0.4260753385290.241833157238-0.1385080294410.371698954114-0.00763650487606-0.2727076364840.332843091322-0.04216410050160.05699745247560.284564966239-0.02558527264740.218903611387-19.564566510325.4675177876-39.6873151962
47.78272489862.178386507151.79474551577.410226585360.7598938341197.85264078702-0.2805273608620.752395700787-0.419652288305-0.5292695483920.54646654247-1.197452803040.004771896337350.939284662092-0.2126033566310.438949412737-0.0981317250550.04545233148040.395774016216-0.1306344157520.372420062412-8.2275289475828.9425614883-39.3874562102
59.338211500250.03995328552241.041562285670.544163925346-0.2205377710520.2229225623110.752107826151-0.114356386338-0.2761317288011.65989877928-0.4338911397311.23607088931.3601211646-0.683673191391-0.6176976370151.03867494156-0.1808085862550.06277981743710.4234410818340.00605489810890.614930506983-12.1156610241.5826180254-29.8976014438
66.631187008261.89362573114-3.728639189655.72092068598-1.778163562925.364462261310.196782172239-0.062684393865-0.832982665690.742075675648-0.546964102285-0.411804169629-0.5524395180390.393530498030.2244295095230.573626819656-0.0891973163005-0.06118912595660.3949538278080.02399911535340.248337979919-18.630685999428.0326287372-21.6150750873
76.04979529486-0.0922103005834-3.333983209685.95972267393-0.3211965466515.65757083463-0.193804625248-0.9389745434690.03425639245631.23512767928-0.4054497247751.267232905950.5204703742130.5314450486210.5174168391190.443416622994-0.07572767057030.1153705963160.408662056835-0.007365039120690.398645559398-35.024670316511.8494201554-18.8029844017
83.0711850185-2.566143548334.082169880011.42199985352-3.054583948028.574271603940.131208458535-0.00141176483840.452665176423-0.08195410436380.0172917989890.297530681192-0.296848227927-0.032722128725-0.0824284345830.477089195376-0.1277702112490.1064975693360.2858485237490.05096652184940.509411045675-26.22060061245.2062099398-11.5269145367
99.32652486068-2.06778528332-2.190914471498.036333363242.775090121691.46821643922-0.2460981784811.052153689720.031171314296-0.256086555705-0.11327232413-0.14418773802-0.0170019181495-0.3897581014330.2439467542350.528388963482-0.0100831386859.22999232733E-50.539779494657-0.05145878370890.245992864573-9.8680238327117.4985105853-7.05635571364
109.481122766911.536708939016.23202059346.952786743026.557366204768.49265299574-0.002617991171890.196208452055-0.0585199533493-0.1774863006710.139066200023-0.0416754897445-0.1587271778680.412668893165-0.1550982334180.428008234952-0.01924117295910.05293450977420.361777472856-0.02330790119140.163596530452-19.270182036324.83409626469.9777443942
113.941151813081.31269449493-2.507671892844.783579784043.261296060544.7994961236-0.07573749699661.381438805930.789164768242-0.5545869583110.43670916756-0.105304081383-0.410404113095-1.0170151303-0.2969269669951.038895357810.1233455772060.01902686059550.9643860970310.08816610614640.376053475447-21.975853907327.9290780069-6.85640573115
124.888229419953.43279569438-2.541323117566.771163435161.488959441033.63944940288-0.6662011080550.676785526987-0.0259446526911-1.698416809640.915397490577-0.790390416480.588774748023-0.401560336072-0.2714007650180.723502141773-0.02632546461850.006507394864650.561971376927-0.09509730171780.749303375044-5.288397164357.44393441613-9.65208633337
133.142782685121.030350965523.676214012090.02687586757580.9861833647613.7755555407-0.0276636794363-0.3632991316610.4547060363570.35183509486-0.260897192175-0.1591499606760.167476127516-0.2742560686850.194059356330.5827639689140.0793848963620.06152828021460.271946472307-0.06472010776850.506516136201-15.00810894274.25455223131-17.635360391
149.582872830021.09456758749-5.665471344387.180263668813.460746160858.83694287962-0.299257654273-0.660503710816-0.0737651491634-0.01367870980740.526641247844-0.3036669725630.8531564137610.371687600099-0.2619448144990.5317514534030.0341421904353-0.01252123688060.2625635250280.01138135007570.192223575977-20.169175696420.1413509903-31.5605230382
156.29028846908-3.95566014563-3.517188407184.22083659414-0.9147272848386.598578117920.05059252644430.211186739733-0.5355752156850.0263470207633-0.1044714854940.0794950145683-0.138660794127-0.0898869540530.02939161842060.516199925213-0.0325600221921-0.04379934177570.339375662402-0.101016904710.30309627749-17.984458772617.0553848676-0.433033856798
168.45852077065-0.5687659904171.294960435193.455429372540.06152540881693.764976609040.04453707266530.244788680360.516519514080.246467711098-0.2593543394750.522189462411-1.0660621903-0.8084254562140.1188055035260.6900158782790.1038175898780.03732333291750.508167731952-0.02242062767140.287756373969-29.226778892931.36575781328.37335331288
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 22 )AA2 - 221 - 21
22chain 'A' and (resid 23 through 39 )AA23 - 3922 - 38
33chain 'A' and (resid 60 through 77 )AA60 - 7759 - 76
44chain 'A' and (resid 78 through 107 )AA78 - 10777 - 106
55chain 'A' and (resid 108 through 112 )AA108 - 112107 - 111
66chain 'B' and (resid 50 through 71 )BB50 - 711 - 22
77chain 'B' and (resid 72 through 92 )BB72 - 9223 - 43
88chain 'B' and (resid 93 through 120 )BB93 - 12044 - 71
99chain 'C' and (resid 2 through 22 )CC2 - 221 - 21
1010chain 'C' and (resid 60 through 77 )CC60 - 7759 - 76
1111chain 'D' and (resid 50 through 74 )DD50 - 741 - 19
1212chain 'D' and (resid 75 through 92 )DD75 - 9220 - 37
1313chain 'D' and (resid 93 through 120 )DD93 - 12038 - 65
1414chain 'A' and (resid 40 through 59 )AA40 - 5939 - 58
1515chain 'C' and (resid 23 through 59)CC23 - 5922 - 58
1616chain 'C' and (resid 78 through 111 )CC78 - 11177 - 110

+
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