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

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Basic information

Entry
Database: PDB / ID: 7qii
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 / homology
Function and homology information


extracellular region / cytoplasm
Similarity search - Function
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
Chaperone protein YscY / Yop proteins translocation protein X
Similarity search - Component
Biological speciesYersinia enterocolitica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.29 Å
AuthorsGilzer, D. / Schreiner, M. / 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


Theoretical massNumber of molelcules
Total (without water)24,9432
Polymers24,9432
Non-polymers00
Water181
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Complex confirmed via co-expression, pull-down, and gelfiltration. Individual expression of either YscX or YscY not possible.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)179.268, 179.268, 41.070
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Space group name HallI4bw2bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: x+1/2,-y,-z+3/4
#5: -x+1/2,y,-z+3/4
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1,x+1/2,z+5/4
#11: y+1,-x+1/2,z+5/4
#12: x+1,-y+1/2,-z+5/4
#13: -x+1,y+1/2,-z+5/4
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2

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Components

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


Mass: 14186.098 Da / Num. of mol.: 1
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: 10757.175 Da / Num. of mol.: 1
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.: 1 / 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

CrystalDensity Matthews: 3.31 Å3/Da / Density % sol: 62.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Protein Concentration: 5 mg/mL; Protein Buffer: 10 mM Tris pH 8.0, 50 mM NaCl, 5 % (w/v) sucrose, 2.5 mM TCEP; Reservoir Solution: 0.1 M Sodium succinate pH 6-6.5, 4.2-4.4 M NaCl, 4 % ...Details: Protein Concentration: 5 mg/mL; Protein Buffer: 10 mM Tris pH 8.0, 50 mM NaCl, 5 % (w/v) sucrose, 2.5 mM TCEP; Reservoir Solution: 0.1 M Sodium succinate pH 6-6.5, 4.2-4.4 M NaCl, 4 % acetonitrile; Drop Ratio: 0.5 - 1 uL Reservoir + 1 uL Protein
PH range: 6 - 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.29→50 Å / Num. obs: 5368 / % possible obs: 99.8 % / Redundancy: 12.7 % / Biso Wilson estimate: 111.44 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.13 / Net I/σ(I): 14.55
Reflection shellResolution: 3.29→3.49 Å / Redundancy: 13 % / Mean I/σ(I) obs: 2.25 / Num. unique obs: 839 / CC1/2: 0.773 / Rrim(I) all: 1.255 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: D_1292118683

Resolution: 3.29→44.82 Å / SU ML: 0.4909 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.2529
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2831 535 9.99 %
Rwork0.2237 4822 -
obs0.2296 5357 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 119.02 Å2
Refinement stepCycle: LAST / Resolution: 3.29→44.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1519 0 0 1 1520
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01211564
X-RAY DIFFRACTIONf_angle_d1.76652122
X-RAY DIFFRACTIONf_chiral_restr0.0879234
X-RAY DIFFRACTIONf_plane_restr0.0125275
X-RAY DIFFRACTIONf_dihedral_angle_d15.6619588
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.29-3.620.31451290.27631166X-RAY DIFFRACTION99.08
3.63-4.150.38151320.25261187X-RAY DIFFRACTION100
4.15-5.220.28121320.23531190X-RAY DIFFRACTION100
5.23-44.820.24831420.19851279X-RAY DIFFRACTION99.86
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)
14.22139703866-0.5044496154522.381190905638.471409293340.978725393721.507835657640.581762559624-0.806380543798-1.19721591390.789076649223-0.6199060001660.8380389194210.402700949604-0.4523687839330.4600896146430.9419375102520.424707279807-0.08828893216811.11764815866-0.2341879379870.45589778375122.4496640283-4.58607721201-3.07012004223
24.73459885708-1.40817622397-4.684784543337.23394203746-0.3064621574765.70569515830.426922131852-0.3602932077172.165618704120.119981648562-0.334410900584-0.826782998309-0.1850561123081.522306905-0.2079868728450.7470471273360.34478437010.001272558661211.19902046485-0.09505712621161.0817680281322.8124859461-5.96472051876-18.4535494497
36.076828925640.951172024793-1.562056459228.119776610362.007994085558.144541122941.11294227911-0.5881039921651.551428905180.5247061642170.842053405612-0.724494120982-0.974977638799-0.633228327798-1.913409245370.992701134219-0.1006262224250.3588298870481.530610328590.07111412156611.3808080505134.3434404638-2.0607908971-24.5393510277
46.20535010982.484876344584.796227477555.684250116323.255377557324.289271087920.4550163699313.052664884082.39656103677-1.63891330310.762919577082-0.727172983975-0.560114753091.644737270241.14963861150.5253255567170.3113900689590.3724979425911.405274936730.1113994669811.5204537742135.9791659656-9.54416210204-29.1083326669
56.26865527496-0.4528996017762.130084402868.61733874219-3.555147446018.18132369855-1.515526022951.174127470882.617961230840.07011195207460.97125702502-3.31596171363-0.545893488248-0.6650735110630.422526665050.7139535776450.3194243088780.03563326777241.587637365150.03208263168551.7531576421239.3697836115-12.4814937479-34.3809406628
66.06860419362-0.68393748184-3.73112298077.76641629778-2.010777467453.26713808929-0.7641643535471.29760756083-1.064101883490.971359197328-0.1045695224820.1145533836031.18945553806-0.6889289321620.5418063207410.827984995607-0.02701582299210.1095019857771.14400877729-0.1878065840261.2239924113624.0858265185-16.664674046-23.9271561943
79.958151329472.028998204723.018636759960.610630535551.152436554552.56321666607-0.066986314098-1.998909105762.375857799841.92644214715-0.3015729885190.400173853850.013168015977-1.56027923773-0.2618374917221.273050177040.1328827825210.06513166634691.02512836763-0.1271987725260.78242730583912.8182985148-4.84099067615-7.00430792092
86.054951318613.19033593795.486295130383.875604636294.316199438395.425936763270.629753496541-1.38469068901-0.232331966031.42257006298-0.7439027253240.3274809572471.61838873331-0.991416230960.1800011566931.077837877060.59951346213-0.01085482080691.095672229490.2634570277111.290758495333.18917100087-4.65123710642-15.0893164136
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 10 through 16 )AA10 - 161 - 7
22chain 'A' and (resid 17 through 64 )AA17 - 648 - 55
33chain 'A' and (resid 65 through 81 )AA65 - 8156 - 72
44chain 'A' and (resid 82 through 98 )AA82 - 9873 - 89
55chain 'A' and (resid 99 through 119 )AA99 - 11990 - 110
66chain 'B' and (resid 47 through 71 )BB47 - 711 - 25
77chain 'B' and (resid 72 through 92 )BB72 - 9226 - 46
88chain 'B' and (resid 93 through 122 )BB93 - 12247 - 76

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