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- PDB-3u66: Crystal structure of T6SS SciP/TssL from Escherichia Coli Enteroa... -

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Basic information

Entry
Database: PDB / ID: 3u66
TitleCrystal structure of T6SS SciP/TssL from Escherichia Coli Enteroaggregative 042
ComponentsPutative type VI secretion proteinType VI secretion system
KeywordsUNKNOWN FUNCTION / Duble helical bundle / Protein secretion / attached to inner membrane
Function / homologyType IV / VI secretion system, DotU / Type IV / VI secretion system, DotU / Type IV / VI secretion system, DotU superfamily / Type VI secretion system protein DotU / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha / membrane / Type VI secretion protein
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.63 Å
AuthorsDurand, E. / Aschtgen, M.S. / Zoued, A. / Spinelli, S. / Watson, P.J.H. / Cambillau, C. / Cascales, E.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structural characterization and oligomerization of the TssL protein, a component shared by bacterial type VI and type IVb secretion systems.
Authors: Durand, E. / Zoued, A. / Spinelli, S. / Watson, P.J. / Aschtgen, M.S. / Journet, L. / Cambillau, C. / Cascales, E.
History
DepositionOct 12, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 9, 2013Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.name / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative type VI secretion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1602
Polymers21,0681
Non-polymers921
Water55831
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Putative type VI secretion protein
hetero molecules

A: Putative type VI secretion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3214
Polymers42,1372
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Buried area3010 Å2
ΔGint-15 kcal/mol
Surface area17480 Å2
MethodPISA
3
A: Putative type VI secretion protein
hetero molecules

A: Putative type VI secretion protein
hetero molecules

A: Putative type VI secretion protein
hetero molecules

A: Putative type VI secretion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,6428
Polymers84,2734
Non-polymers3684
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
Buried area11400 Å2
ΔGint-65 kcal/mol
Surface area29570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.610, 82.030, 96.080
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Putative type VI secretion protein / Type VI secretion system / SciP/TssL


Mass: 21068.330 Da / Num. of mol.: 1 / Fragment: Cytoplasmic domain, residues 1-183
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: EAEC 042 / Gene: EC042_4527, SciP/TssL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 PLys / References: UniProt: D3GU40
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 2.41 Å3/Da / Density % sol: 49.03 %
Crystal growTemperature: 273 K / Method: vapor diffusion, sitting drop / pH: 10.6
Details: mixing 300 nL protein at 23mg/mL with 100 nL 4.3 M NaCl, 0.1 M Bicine pH 10.6. , VAPOR DIFFUSION, SITTING DROP, temperature 273K

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Data collection

Diffraction
IDCrystal-ID
11
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID14-410.9791
SYNCHROTRONSOLEIL PROXIMA 120.9791
Detector
TypeIDDetectorDate
ADSC QUANTUM 315r1CCDAug 26, 2011
PSI PILATUS 6M2PIXELSep 21, 2011
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1mirrorsSINGLE WAVELENGTHMx-ray1
2mirrorsSINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.63→45 Å / Num. all: 11601 / Num. obs: 11601 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Biso Wilson estimate: 70.17 Å2 / Rmerge(I) obs: 0.056 / Rsym value: 0.056 / Net I/σ(I): 20.2
Reflection shellResolution: 2.63→2.7 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.5 / Num. unique all: 853 / Rsym value: 0.6 / % possible all: 99.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXDphasing
PHASERphasing
BUSTER2.9.2refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.63→43.68 Å / Cor.coef. Fo:Fc: 0.899 / Cor.coef. Fo:Fc free: 0.8874 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2573 604 9.62 %RANDOM
Rwork0.2353 ---
all0.2375 6278 --
obs0.2375 6278 --
Displacement parametersBiso mean: 69.84 Å2
Baniso -1Baniso -2Baniso -3
1-12.7739 Å20 Å20 Å2
2--8.7743 Å20 Å2
3----21.5482 Å2
Refine analyzeLuzzati coordinate error obs: 0.414 Å
Refinement stepCycle: LAST / Resolution: 2.63→43.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1288 0 6 31 1325
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0091321HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.071795HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d22.04439SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes027HARMONIC2
X-RAY DIFFRACTIONt_gen_planes0197HARMONIC5
X-RAY DIFFRACTIONt_it01321HARMONIC20
X-RAY DIFFRACTIONt_omega_torsion2.36
X-RAY DIFFRACTIONt_other_torsion22.04
X-RAY DIFFRACTIONn_angle_d0171SEMIHARMONIC5
X-RAY DIFFRACTIONn_bond_d01534SEMIHARMONIC4
LS refinement shellResolution: 2.63→2.94 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.323 167 9.58 %
Rwork0.2652 1576 -
all0.2706 1743 -
obs-853 -
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)
10.0428-0.088-0.07990.0878-0.0250.04960.0003-0.0015-0.00020-0.0013-0.0014-0.00130.00240.0010.00120.00350.0003-0.00350.0005-0.000226.60014.728830.172
20.04080.0162-0.18310.0734-0.22010.24160.0009-0.00150.00080.0019-0.0024-0.004-0.00620.00580.00150.0042-0.00450.00280.00430.0050.002728.120613.949623.0117
30.20330.0037-0.31570.14340.15810.14630.00020.0040.0014-0.0012-0.00050.0028-0.0015-0.00410.00030.0007-0.00270.0017-0.0005-0.00140.002422.0914.277332.7485
400.0829-0.01870.00340.03420-0.0003-0.00140.00020.00240-0.00030.00060.00220.0002-0.0014-0.00760.0002-0.0030.0007-0.000926.803421.514235.1746
50-0.0610.046100.012900-0.00080.0006-0.000900.002200.00010-0.00370.00340.0024-0.0018-0.0011-0.0027.316315.817630.0354
600.01690.00310-0.01840-0.0001-0.0012-0.00090.000200.0004-0.00030.00020.0001-0.003-0.00350.0006-0.0021-0.0003-0.003714.94617.168331.4774
70.0009-0.0108-0.00110.01250.00240.00880-0.00010.0003-0.0002-0.00010.00110-0.00060.00010.0005-0.00040.00110.0015-0.00050.00166.518818.827242.7398
800.0417-0.041500.00590-0.0001-0.0009-0.00040.00050.00050.00140-0.0012-0.0004-0.0043-0.0070.0018-0.00330.0005-0.00015.52165.7434.5899
90.05230.0108-0.02840.03770.00810.007-0.0001-0.00050.00030.00140.0003-0.00030.00030-0.00020.0014-0.0016-0.00130.00270.000309.5908-1.605249.5172
100.0076-0.0043-0.00350.0084-0.00220.00570.0001-0.00020.00020.000200-0.0005000.00290.0001-0.00010.0017-0.00070.002412.23836.600467.5071
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|6 - A|32}A6 - 32
2X-RAY DIFFRACTION2{A|33 - A|57}A33 - 57
3X-RAY DIFFRACTION3{A|58 - A|79}A58 - 79
4X-RAY DIFFRACTION4{A|85 - A|104}A85 - 104
5X-RAY DIFFRACTION5{A|105 - A|121}A105 - 121
6X-RAY DIFFRACTION6{A|122 - A|137}A122 - 137
7X-RAY DIFFRACTION7{A|138 - A|145}A138 - 145
8X-RAY DIFFRACTION8{A|146 - A|163}A146 - 163
9X-RAY DIFFRACTION9{A|164 - A|172}A164 - 172
10X-RAY DIFFRACTION10{A|173 - A|178}A173 - 178

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