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- PDB-6sjt: Crystal structure of the Legionella pneumophila type II secretion... -

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Basic information

Entry
Database: PDB / ID: 6sjt
TitleCrystal structure of the Legionella pneumophila type II secretion system substrate NttC
ComponentsNttC
KeywordsUNKNOWN FUNCTION / Legionella pneumophila / type II sectorion system
Function / homologyUncharacterized protein
Function and homology information
Biological speciesLegionella pneumophila 130b (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.103 Å
AuthorsPortlock, T.J. / Rehman, S. / Garnett, J.A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MR/M009920/10 United Kingdom
CitationJournal: Front Mol Biosci / Year: 2020
Title: Structure, Dynamics and Cellular Insight Into Novel Substrates of theLegionella pneumophilaType II Secretion System.
Authors: Portlock, T.J. / Tyson, J.Y. / Dantu, S.C. / Rehman, S. / White, R.C. / McIntire, I.E. / Sewell, L. / Richardson, K. / Shaw, R. / Pandini, A. / Cianciotto, N.P. / Garnett, J.A.
History
DepositionAug 13, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 20, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2020Group: 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 1.2Oct 23, 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
AAA: NttC
BBB: NttC


Theoretical massNumber of molelcules
Total (without water)27,2352
Polymers27,2352
Non-polymers00
Water181
1
AAA: NttC


Theoretical massNumber of molelcules
Total (without water)13,6181
Polymers13,6181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: NttC


Theoretical massNumber of molelcules
Total (without water)13,6181
Polymers13,6181
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.390, 84.390, 151.660
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11AAA-201-

HOH

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Components

#1: Protein NttC


Mass: 13617.553 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila 130b (bacteria) / Gene: lpw18401 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0C9MKT2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 3.34 Å3/Da / Density % sol: 63.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 3.5 M ammonium chloride, 100 mM Tris-HCl pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9796, 0.9797, 0.9681
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 8, 2013
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97961
20.97971
30.96811
ReflectionResolution: 3.1→73.084 Å / Num. obs: 6280 / % possible obs: 100 % / Redundancy: 20.4 % / Biso Wilson estimate: 56.2 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.283 / Rpim(I) all: 0.064 / Rrim(I) all: 0.29 / Net I/σ(I): 10.1
Reflection shellResolution: 3.1→3.18 Å / Redundancy: 20.9 % / Rmerge(I) obs: 1.022 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 437 / CC1/2: 0.933 / Rpim(I) all: 0.226 / Rrim(I) all: 1.048 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
XDSdata reduction
Aimlessdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 3.103→73.084 Å / Cor.coef. Fo:Fc: 0.885 / Cor.coef. Fo:Fc free: 0.888 / WRfactor Rfree: 0.276 / WRfactor Rwork: 0.244 / SU B: 50.593 / SU ML: 0.372 / Average fsc free: 0.8877 / Average fsc work: 0.9134 / Cross valid method: FREE R-VALUE / ESU R: 0.975 / ESU R Free: 0.476
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2886 303 4.848 %
Rwork0.2502 5947 -
all0.252 --
obs-6250 99.984 %
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 59.913 Å2
Baniso -1Baniso -2Baniso -3
1--0.307 Å2-0.154 Å20 Å2
2---0.307 Å20 Å2
3---0.996 Å2
Refinement stepCycle: LAST / Resolution: 3.103→73.084 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1626 0 0 1 1627
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0131664
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171490
X-RAY DIFFRACTIONr_angle_refined_deg1.2811.6682282
X-RAY DIFFRACTIONr_angle_other_deg1.0811.5643470
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6115214
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.07823.42970
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.82315236
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.478156
X-RAY DIFFRACTIONr_chiral_restr0.0380.2242
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021880
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02314
X-RAY DIFFRACTIONr_nbd_refined0.1830.2266
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1750.21326
X-RAY DIFFRACTIONr_nbtor_refined0.1520.2817
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.070.2757
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.231
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1810.210
X-RAY DIFFRACTIONr_nbd_other0.2190.241
X-RAY DIFFRACTIONr_ncsr_local_group_10.0810.053227
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
3.103-3.1840.344300.3254070.3274370.810.8521000.299
3.184-3.2710.453160.3074210.3124370.8360.8661000.278
3.271-3.3650.352180.2984020.34200.8320.8851000.272
3.365-3.4690.339160.2793990.2814150.8620.8991000.248
3.469-3.5820.337190.2893750.2913940.8570.8881000.271
3.582-3.7080.318230.2713650.2743880.8550.9021000.25
3.708-3.8470.256240.2863660.2843900.9320.8951000.263
3.847-4.0040.275210.253290.2523500.920.9131000.234
4.004-4.1810.522130.2493320.2553450.7650.9161000.234
4.181-4.3850.279140.2253260.2273400.8780.9391000.215
4.385-4.6210.193220.2213010.2193230.960.9441000.218
4.621-4.90.301180.1752890.1823070.9460.9641000.177
4.9-5.2370.183130.2352820.2332950.9590.9461000.222
5.237-5.6540.325110.2322610.2362720.9290.9391000.22
5.654-6.190.312110.2522390.2562500.9360.9321000.244
6.19-6.9140.39180.2512290.2542370.860.931000.247
6.914-7.9720.312130.2141970.2212100.9210.951000.221
7.972-9.7350.15660.191760.1881820.9830.9681000.202
9.735-13.6470.25230.1941520.1951550.9640.9771000.212
13.647-73.0840.29840.395990.3921040.9640.90599.03850.653
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)
14.8825-0.9708-0.94734.35491.14325.3370.08570.065-0.33250.433-0.0691-0.05690.23150.4527-0.01650.0634-0.0146-0.02130.6103-0.10830.047730.7443.58614.794
25.3003-0.61942.3792.76182.14966.4345-0.01930.57280.1005-0.0367-0.15260.1347-0.8839-0.42470.17190.23350.09810.03260.6003-0.11220.17519.61613.0677.934
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA*1 - 108
2X-RAY DIFFRACTION2ALLB*1 - 108

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