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- PDB-6xrb: Crystal structure of SciW from Salmonella typhimurium -

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Basic information

Entry
Database: PDB / ID: 6xrb
TitleCrystal structure of SciW from Salmonella typhimurium
Components(SciW) x 2
KeywordsCHAPERONE / SciW / Type VI secretion / T6SS
Function / homologyInner membrane lipoprotein DcrB/EagT6 / DcrB / Mog1/PsbP, alpha/beta/alpha sandwich / Protein Transport Mog1p; Chain A / Mog1/PsbP, alpha/beta/alpha sandwich / 3-Layer(aba) Sandwich / Alpha Beta / TRIETHYLENE GLYCOL / DUF1795 domain-containing protein
Function and homology information
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsSachar, K. / Ahmad, S. / Whitney, J.C. / Prehna, G.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2018-04968 Canada
CitationJournal: Elife / Year: 2020
Title: Structural basis for effector transmembrane domain recognition by type VI secretion system chaperones.
Authors: Ahmad, S. / Tsang, K.K. / Sachar, K. / Quentin, D. / Tashin, T.M. / Bullen, N.P. / Raunser, S. / McArthur, A.G. / Prehna, G. / Whitney, J.C.
History
DepositionJul 11, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SciW
B: SciW
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2733
Polymers34,1232
Non-polymers1501
Water4,594255
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3930 Å2
ΔGint-12 kcal/mol
Surface area16120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.269, 75.093, 76.599
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein SciW


Mass: 17023.201 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (strain SL1344) (bacteria)
Strain: SL1344 / Gene: sciW, SL1344_0285
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A0H3NHS6
#2: Protein SciW


Mass: 17099.320 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (strain SL1344) (bacteria)
Strain: SL1344 / Gene: sciW, SL1344_0285
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A0H3NHS6
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 255 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.33 Å3/Da / Density % sol: 47.19 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 22 mg/mL SciW with a 1:1 mixture of 0.1 M Tris HCL pH 8.5, 25% (v/v) PEG 550 MME

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.75→26.81 Å / Num. obs: 32309 / % possible obs: 99.5 % / Redundancy: 6.95 % / Biso Wilson estimate: 31.23 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.071 / Net I/σ(I): 14.23
Reflection shellResolution: 1.75→1.85 Å / Num. unique obs: 5091 / CC1/2: 0.891 / Rrim(I) all: 0.93 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
Cootmodel building
PHENIXmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.76→26.81 Å / SU ML: 0.2274 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.1828
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2246 1613 4.99 %
Rwork0.1989 30681 -
obs0.2002 32294 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.06 Å2
Refinement stepCycle: LAST / Resolution: 1.76→26.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2322 0 10 256 2588
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00312393
X-RAY DIFFRACTIONf_angle_d0.66763245
X-RAY DIFFRACTIONf_chiral_restr0.0436355
X-RAY DIFFRACTIONf_plane_restr0.0031431
X-RAY DIFFRACTIONf_dihedral_angle_d15.1814904
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.76-1.810.37531260.33642465X-RAY DIFFRACTION97.74
1.81-1.870.31881330.30512526X-RAY DIFFRACTION99.74
1.87-1.930.29751320.2812513X-RAY DIFFRACTION99.62
1.93-2.010.28691340.24072550X-RAY DIFFRACTION99.85
2.01-2.10.23951330.23372522X-RAY DIFFRACTION99.96
2.1-2.210.21551340.20572554X-RAY DIFFRACTION99.89
2.21-2.350.28941330.2052519X-RAY DIFFRACTION99.47
2.35-2.530.25151360.21332555X-RAY DIFFRACTION99.37
2.53-2.790.26181340.21482557X-RAY DIFFRACTION99.41
2.79-3.190.22681360.20472574X-RAY DIFFRACTION99.49
3.19-4.020.21131370.17582611X-RAY DIFFRACTION99.93
4.02-26.810.17851450.17252735X-RAY DIFFRACTION99.69
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)
17.96677120799-3.469705530752.851258367739.28320551159-3.675320299552.742691469740.8460919677431.91711916095-0.780876089535-1.25790620942-0.9742467014360.6386255067090.60368409006-1.070431266520.3037983917190.4350765456690.0480766685989-0.09576013858630.508633263923-0.1182270110180.567732569324-32.12651953463.2628977862315.6203613549
26.06557447504-6.472737415324.082937816098.00674674882-3.608102438816.93730526888-0.184892176869-0.100047336388-0.1450818860580.4417275106580.1658277044140.0441562710489-0.235426679959-0.3994356029650.02834878521480.276202370878-0.0337588008909-0.009203999645220.278789266343-0.05384090181310.314186095499-22.9431040747-5.5458226639518.5773463224
39.49998920839-6.036356016962.312598253754.60443937774-2.387724286096.15021635996-0.02784923437320.320562162880.07930137926640.0174583577653-0.04797578678090.04473819628170.09823261084620.158009641251-0.06547608541860.230411418208-0.038313970417-0.09171295413510.347486812363-0.06652640622190.295967530458-18.2795930337-12.953352319111.1829387109
43.241717366130.647761617038-0.5692450056515.292591293010.8762004405354.23099560578-0.1834652861620.318663216973-0.0251695775422-0.6757437372640.181677522703-0.338694752434-0.1217332752680.1419750867040.02689873474110.297866176907-0.0338883515011-0.04526657367950.213937525314-0.01693495037560.300843481976-21.5383734473-25.15507595543.49756082314
55.63085511397-0.254023854395-2.960891050292.915408829351.414219844927.50315715518-0.221959900089-0.185752698419-0.4346943324950.1973206385820.307163196113-0.3445703963210.450530961680.1923214420920.02291869018380.21001499819-0.0184003790406-0.02229474074120.2198291816770.001493561967930.313426440487-25.3681924175-30.929803284614.2150953993
66.268435337422.60483802292-1.383268670015.26769582938-1.062836333515.282726806810.254703327237-0.454801589483-0.314333567850.552861103655-0.0796028971987-0.01502663787490.2701481992150.207893381646-0.09064685175860.337469753381-0.010060341783-0.07345011783610.237924144533-0.07854266202550.306793724417-19.5956208493-16.564375966118.3813317943
74.040783405890.0762664797511-1.808630259294.337775181220.36688449211.31304206396-0.00128346816567-0.129978778321-0.182356370618-0.05959392631330.0798662168001-0.3994946078750.05763452746440.142042285831-0.1128602353620.307310454437-0.00129729828126-0.05792661721130.333824045478-0.04153623141710.306996468642-5.94615908165-4.8881341694215.6385773565
85.09770841081-1.15080352047-4.31806678943.366536001881.840956647016.308290549120.373821923954-0.2692487236780.141934286267-0.2819652426160.363536987901-0.742905894677-0.05375366901010.850446340682-0.3945613271990.385461097294-0.0172845010027-0.0816662037910.372354763546-0.09145652911480.4492643776932.170276166941.692113661612.3307066049
93.23290559761-1.23901002848-1.845236561532.148321821661.067630692724.561991482250.0825873917279-0.0752514088414-0.00606002533872-0.002767650191670.078374899019-0.18054148371-0.02072438705350.103604891317-0.143212776720.240417535776-0.021717452332-0.06346196357140.284103898264-0.03194703117370.315158830064-8.55363989590.5005465169817.1067852745
107.531823733891.5175923584-4.904675788438.21177000104-0.687772922158.531157971280.1614086180970.05032713845570.412039870171-0.31276493913-0.06652670757740.0230185976448-0.340300608615-0.237595805215-0.2585163640080.2640081232820.0505495714593-0.06778191080670.278652642125-0.03400069598260.26599170291-16.28846012895.3498015639816.4525822906
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid -4:4)
2X-RAY DIFFRACTION2(chain A and resid 5:15)
3X-RAY DIFFRACTION3(chain A and resid 16:30)
4X-RAY DIFFRACTION4(chain A and resid 31:124)
5X-RAY DIFFRACTION5(chain A and resid 125:145)
6X-RAY DIFFRACTION6(chain B and resid 1:28)
7X-RAY DIFFRACTION7(chain B and resid 29:61)
8X-RAY DIFFRACTION8(chain B and resid 62:76)
9X-RAY DIFFRACTION9(chain B and resid 77:124)
10X-RAY DIFFRACTION10(chain B and resid 125:146)

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