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- PDB-6uid: Structure of the cytoplasmic domain of the T3SS sorting platform ... -

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Basic information

Entry
Database: PDB / ID: 6uid
TitleStructure of the cytoplasmic domain of the T3SS sorting platform protein PscD from P. aeruginosa
ComponentsEscD/YscD/HrpQ family type III secretion system inner membrane ring protein
KeywordsPROTEIN BINDING / PscD / type III secretion apparatus protein
Function / homology
Function and homology information


protein secretion by the type III secretion system / membrane
Similarity search - Function
Yop protein translocation protein D, periplasmic domain / : / : / YscD/CdsD-like Bon-like domain 1 / YscD/CdsD-like Bon-like domain 3 / YscD/CdsD-like Bon-like domain 2 / Type III secretion system YscD/HrpQ / YscD, cytoplasmic domain / Inner membrane component of T3SS, cytoplasmic domain
Similarity search - Domain/homology
: / Type III export protein PscD
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.45 Å
AuthorsMuthuramalingam, M. / Lovell, S. / Battaile, K.P. / Picking, W.D.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI123351 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21 AI146517 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30 GM110761 United States
CitationJournal: J.Mol.Biol. / Year: 2020
Title: The Structures of SctK and SctD from Pseudomonas aeruginosa Reveal the Interface of the Type III Secretion System Basal Body and Sorting Platform.
Authors: Muthuramalingam, M. / Whittier, S.K. / Lovell, S. / Battaile, K.P. / Tachiyama, S. / Johnson, D.K. / Picking, W.L. / Picking, W.D.
History
DepositionSep 30, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 4, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 11, 2020Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Dec 16, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: EscD/YscD/HrpQ family type III secretion system inner membrane ring protein


Theoretical massNumber of molelcules
Total (without water)13,6861
Polymers13,6861
Non-polymers00
Water2,774154
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.086, 48.086, 235.509
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-343-

HOH

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Components

#1: Protein EscD/YscD/HrpQ family type III secretion system inner membrane ring protein


Mass: 13686.382 Da / Num. of mol.: 1 / Fragment: cytosolic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: FAZ09_09230 / Plasmid: pT7HMT / Production host: Escherichia coli (E. coli) / Strain (production host): Tuner (DE3) / References: UniProt: A0A4U0JQ60, UniProt: Q9I318*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 2.87 Å3/Da / Density % sol: 57.16 % / Mosaicity: 0.09 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.9
Details: 1.8 M sodium phosphate monobasic monohydrate, potassium phosphate dibasic

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→47.1 Å / Num. obs: 29928 / % possible obs: 99.6 % / Redundancy: 13.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.069 / Net I/σ(I): 18.9 / Num. measured all: 415491
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Net I/σ(I) obs% possible all
1.45-1.475.60.912748913430.7381.795.4
7.94-47.111.70.0383177272144.499.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.32data scaling
PHENIX1.14_3237refinement
PDB_EXTRACT3.25data extraction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4A0E

4a0e


Resolution: 1.45→33.999 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.19 / Phase error: 18.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1983 1461 4.91 %
Rwork0.1685 28319 -
obs0.1699 29780 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 82.84 Å2 / Biso mean: 22.5652 Å2 / Biso min: 10.86 Å2
Refinement stepCycle: final / Resolution: 1.45→33.999 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms886 0 0 154 1040
Biso mean---33.73 -
Num. residues----120
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.45-1.50190.29811400.2782267696
1.5019-1.5620.24871450.2219270499
1.562-1.63310.19311350.18482778100
1.6331-1.71920.19681550.16742788100
1.7192-1.82690.17841510.16122751100
1.8269-1.96790.19481330.15592836100
1.9679-2.16590.18711360.15242841100
2.1659-2.47930.18321680.16072852100
2.4793-3.12330.19211420.17252927100
3.1233-33.9990.20351560.16423166100
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)
10.1367-0.0764-0.21090.2374-0.12810.41030.071-0.16490.22640.0681-0.04230.0826-0.0530.0365-0.00010.1114-0.0146-0.00420.17220.01030.1535-7.578830.33319.1292
20.11050.03070.24660.16140.5190.55730.0165-0.00550.07340.13940.01310.06380.033-0.03430.00010.1201-0.00660.00370.15680.00330.1397-0.330423.029613.7843
30.0681-0.0658-0.07790.19720.01280.15250.013-0.0119-0.15490.07030.0383-0.0120.1921-0.0334-0.00020.1776-0.0158-0.00820.19670.0050.1728-9.459719.233314.204
40.1713-0.29310.11490.3705-0.06920.4568-0.04040.0763-0.0468-0.01970.0472-0.01870.06340.0291-00.1308-0.01170.00130.169-0.00850.1398-0.662918.3735.3843
50.1764-0.1233-0.18970.08410.13530.07330.02440.3105-0.0898-0.1566-0.06930.1066-0.0383-0.0256-0.00020.1302-0.0013-0.00450.2073-0.01830.1385-2.373922.788-3.8886
60.659-0.00770.1790.03230.00290.42440.0075-0.00240.1584-0.0153-0.06560.0036-0.05780.0012-00.1016-0.008-0.00580.1486-0.00040.1754-7.059430.23782.9237
70.0434-0.06660.15190.1418-0.21020.30160.08760.0475-0.00810.1470.00850.08260.10760.0891-00.1583-0.01050.00390.1688-0.01030.1309-20.325716.207-14.3743
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 15 )A1 - 15
2X-RAY DIFFRACTION2chain 'A' and (resid 16 through 31 )A16 - 31
3X-RAY DIFFRACTION3chain 'A' and (resid 32 through 41 )A32 - 41
4X-RAY DIFFRACTION4chain 'A' and (resid 42 through 66 )A42 - 66
5X-RAY DIFFRACTION5chain 'A' and (resid 67 through 84 )A67 - 84
6X-RAY DIFFRACTION6chain 'A' and (resid 85 through 106 )A85 - 106
7X-RAY DIFFRACTION7chain 'A' and (resid 107 through 120 )A107 - 120

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