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- PDB-7qih: Complex of the Yersinia enterocolitica Type III secretion protein... -

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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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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


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

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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: 1.93 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

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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

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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

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