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- PDB-3uep: Crystal structure of YscQ-C from Yersinia pseudotuberculosis -

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Basic information

Entry
Database: PDB / ID: 3uep
TitleCrystal structure of YscQ-C from Yersinia pseudotuberculosis
ComponentsYscQ-C, type III secretion protein
KeywordsPROTEIN TRANSPORT / type III secretion protein / cytosol
Function / homology
Function and homology information


protein secretion by the type III secretion system / :
Similarity search - Function
Surface presentation of antigens (SPOA) / SpoA-like / Type III secretion system apparatus protein YscQ/HrcQ/SpaO / Type III secretion system outer membrane, SpaO / Flagellar motor switch protein FliN-like, C-terminal domain / SpoA-like superfamily / Type III flagellar switch regulator (C-ring) FliN C-term / Roll / Mainly Beta
Similarity search - Domain/homology
Yop proteins translocation protein Q
Similarity search - Component
Biological speciesYersinia pseudotuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsBzymek, K.P. / Ghosh, P.
CitationJournal: Biochemistry / Year: 2012
Title: Two Translation Products of Yersinia yscQ Assemble To Form a Complex Essential to Type III Secretion.
Authors: Bzymek, K.P. / Hamaoka, B.Y. / Ghosh, P.
History
DepositionOct 31, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: YscQ-C, type III secretion protein
B: YscQ-C, type III secretion protein


Theoretical massNumber of molelcules
Total (without water)21,4042
Polymers21,4042
Non-polymers00
Water90150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4260 Å2
ΔGint-32 kcal/mol
Surface area10480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.130, 114.130, 88.560
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein YscQ-C, type III secretion protein


Mass: 10702.135 Da / Num. of mol.: 2
Fragment: C-terminal fragment from internal translation initiation site (UNP residues 220-307)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pseudotuberculosis (bacteria) / Strain: 126 / Gene: pYV virulence plasmid, pYV0070, yscQ / Plasmid: pET28b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P40296
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 2.59 Å3/Da / Density % sol: 52.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.8
Details: 100 mM Tris, 1.5 M ammonium sulfate, pH 8.8, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.9686 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 7, 2009
RadiationMonochromator: Double crystal cryo-cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.25→34.42 Å / Num. all: 10671 / Num. obs: 10594 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 10.8 % / Biso Wilson estimate: 46.13 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 32.1
Reflection shellResolution: 2.25→2.31 Å / Redundancy: 9.8 % / Rmerge(I) obs: 0.232 / Mean I/σ(I) obs: 10.45 / Num. unique all: 730 / % possible all: 94.2

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Processing

Software
NameVersionClassification
HKL-3000data collection
MOLREPphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Se-Met YscQ-C (I248M)

Resolution: 2.25→34.421 Å / SU ML: 0.61 / Cross valid method: THROUGHOUT / σ(F): 2.04 / Phase error: 27.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2332 530 5 %RANDOM
Rwork0.2018 ---
obs0.2035 10592 99.28 %-
all-10592 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.276 Å2 / ksol: 0.36 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.9384 Å2-0 Å2-0 Å2
2---3.9384 Å2-0 Å2
3---7.8768 Å2
Refinement stepCycle: LAST / Resolution: 2.25→34.421 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1320 0 0 50 1370
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091395
X-RAY DIFFRACTIONf_angle_d1.2441906
X-RAY DIFFRACTIONf_dihedral_angle_d14.614540
X-RAY DIFFRACTIONf_chiral_restr0.08237
X-RAY DIFFRACTIONf_plane_restr0.004245
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2504-2.47680.32371290.26622458X-RAY DIFFRACTION98
2.4768-2.83510.26991320.25452505X-RAY DIFFRACTION100
2.8351-3.57130.25271330.20232528X-RAY DIFFRACTION100
3.5713-34.42460.19571360.17562571X-RAY DIFFRACTION99
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)
11.5144-0.77550.39166.21340.57271.14-0.04280.40790.0133-0.8236-0.1983-0.41550.05330.20210.28420.2798-0.00660.05520.16770.00370.2029-24.4242.8481-31.7818
23.846-3.5164-5.10433.31264.63846.7804-0.93950.0010.560.77421.4110.4525-0.318-0.706-0.44180.45160.09890.02820.56760.13860.3951-14.3895-22.8324-23.9903
38.18450.22644.31172.6526-1.22953.17370.33720.69190.15430.2897-0.2745-0.12290.26480.4517-0.06090.24620.01510.00470.1414-0.06990.1265-14.2847-29.2695-31.7132
46.31154.63170.07815.35360.10638.02460.6275-0.45681.30680.3166-0.01211.3941-1.2308-0.8773-0.57720.7080.3410.37240.9050.40550.8671-28.3988-22.6391-21.2309
52.7634-0.2854-0.18924.97251.68781.25980.00940.1762-0.1433-0.30450.1073-0.8601-0.19040.0545-0.0180.45120.29010.1224-0.1429-0.150.2423-21.8617-10.1759-23.888
69.7674.7551-0.25043.94460.8822.0985-0.0154-0.0185-0.51140.364-0.0563-0.1304-0.0095-0.64850.14440.36260.06760.00960.3836-0.01350.2731-28.7871-11.6773-22.9854
78.58842.17293.49998.93684.99853.8395-0.2050.2268-0.28640.2695-0.35020.7685-0.1888-0.72660.57740.2519-0.0130.08980.360.00960.2413-32.7704-10.551-23.1023
83.21050.80120.3675.132-4.56734.5061-0.23230.1217-0.49420.5801-0.0589-1.2518-0.44430.0039-0.15430.3975-0.0990.04820.2146-0.05020.3001-17.5817.5585-29.2128
92.38740.3593-0.67387.0247-0.77576.9411-0.2524-0.86350.08720.8499-0.082-0.34190.00980.63760.30620.25740.0001-0.09130.318-0.0730.1699-1.9222-26.2945-23.4033
104.7701-1.6658-2.1035.74210.21344.72030.12050.2583-0.1083-0.0121-0.07410.5214-0.1267-0.0994-0.02550.20730.0589-0.00990.16270.03110.2112-29.1825-6.881-29.0515
117.6251-1.5397-1.64068.0461-1.57115.34840.12-0.06570.27520.33790.0590.77090.0643-0.2254-0.17550.27910.08140.09480.0906-0.01880.1573-21.9205-22.9238-33.4898
127.56531.81035.13881.4261.7585.9884-0.28840.26331.1551-0.6787-0.42240.2719-0.49560.03530.48130.1512-0.0201-0.14630.15430.05380.4163-0.5837-18.8594-29.0892
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 229:244)
2X-RAY DIFFRACTION2chain 'A' and (resseq 245:250)
3X-RAY DIFFRACTION3chain 'A' and (resseq 251:265)
4X-RAY DIFFRACTION4chain 'A' and (resseq 266:271)
5X-RAY DIFFRACTION5chain 'A' and (resseq 272:279)
6X-RAY DIFFRACTION6chain 'A' and (resseq 280:290)
7X-RAY DIFFRACTION7chain 'A' and (resseq 291:301)
8X-RAY DIFFRACTION8chain 'A' and (resseq 302:313)
9X-RAY DIFFRACTION9chain 'B' and (resseq 229:239)
10X-RAY DIFFRACTION10chain 'B' and (resseq 240:271)
11X-RAY DIFFRACTION11chain 'B' and (resseq 272:301)
12X-RAY DIFFRACTION12chain 'B' and (resseq 302:313)

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