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

ID or keywords:

Entry

Database: PDB / ID: 6skw

Title

Crystal structure of the Legionella pneumophila type II secretion system substrate NttE

Components

NttE

Keywords

UNKNOWN FUNCTION / Legionella pneumophila / type II secretion system

Function / homology

Uncharacterized protein

Function and homology information

Biological species

Legionella pneumophila 130b (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.2 Å

Authors

Portlock, T.J. / Rehman, S. / Garnett, J.A.

Funding support

United Kingdom, 1items

Citation

Journal: 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

Deposition	Aug 16, 2019	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 20, 2020	Provider: repository / Type: Initial release
Revision 1.1	Jul 22, 2020	Group: 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 1.2	Nov 13, 2024	Group: 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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6skw.cif.gz	220.6 KB	Display	PDBx/mmCIF format
PDB format	pdb6skw.ent.gz		Display	PDB format
PDBx/mmJSON format	6skw.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	6skw_validation.pdf.gz	2.5 MB	Display	wwPDB validaton report
Full document	6skw_full_validation.pdf.gz	2.5 MB	Display
Data in XML	6skw_validation.xml.gz	24.6 KB	Display
Data in CIF	6skw_validation.cif.gz	35.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/sk/6skw ftp://data.pdbj.org/pub/pdb/validation_reports/sk/6skw	HTTPS FTP

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Related structure data

Related structure data	6sjtC 6xttC C: citing same article (ref.)
Similar structure data	5a89-d 6x9n-3 5ay6-1 5k5d-2 4d5s-2 7cbs-3 1ixz-d 2r65-1 3d5n-1 5k5d-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#211 - Jul 2017 Pilus Machine similarity (1)

Deposited unit

AAA: NttE

BBB: NttE

hetero molecules

67.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

AAA: NttE

hetero molecules

defined by author
Evidence: gel filtration
34 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

BBB: NttE

hetero molecules

defined by author
33.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	120.870, 120.870, 104.390
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	154
Space group name H-M	P3₂21

Components on special symmetry positions

ID	Model	Components
1	1	AAA-517- HOH

#1: Protein	NttE Mass: 33611.949 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Legionella pneumophila 130b (bacteria) / Gene: D7214_10670, DIZ48_11715, DIZ50_11270 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A4Q5N6R9
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C₂H₆O₂ / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 344 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 3.32 Å³/Da / Density % sol: 62.91 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 40% (v/v) ethylene glycol, 20% (w/v) polyethylene glycol 8000, 50 mM imidazole, 50 mM 2-(N-morpholine)ethanesulfonic acid pH 6.5, 300 mM magnesium chloride, 300 mM calcium chloride

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9793 Å
Detector	Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 23, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9793 Å / Relative weight: 1
Reflection	Resolution: 2.2→104.68 Å / Num. obs: 45011 / % possible obs: 99.9 % / Redundancy: 13.9 % / B_iso Wilson estimate: 36.5 Å² / R_merge(I) obs: 0.071 / R_pim(I) all: 0.024 / R_rim(I) all: 0.09 / Net I/σ(I): 25.1
Reflection shell	Resolution: 2.2→2.26 Å / R_merge(I) obs: 0.423 / Mean I/σ(I) obs: 7.2 / Num. unique obs: 3292 / R_pim(I) all: 0.121 / R_rim(I) all: 0.46 / % possible all: 99.5

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0253	refinement
XDS		data reduction
SCALA		data scaling
SHARP		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.2→104.676 Å / Cor.coef. F_o:F_c: 0.953 / Cor.coef. F_o:F_c free: 0.936 / Cross valid method: FREE R-VALUE / ESU R: 0.187 / ESU R Free: 0.157
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2105	2273	5.05 %
R_work	0.1867	-	-
all	0.188	-	-
obs	-	45010	99.834 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 38.96 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.145 Å²	0.573 Å²	0 Å²
2-	-	1.145 Å²	0 Å²
3-	-	-	-3.716 Å²

Refinement step

Cycle: LAST / Resolution: 2.2→104.676 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4330	0	44	345	4719

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.013	4491
X-RAY DIFFRACTION	r_bond_other_d	0.034	0.017	3935
X-RAY DIFFRACTION	r_angle_refined_deg	1.698	1.661	6076
X-RAY DIFFRACTION	r_angle_other_deg	2.296	1.57	9179
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.583	5	528
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.619	23.864	264
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.893	15	698
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.094	15	20
X-RAY DIFFRACTION	r_chiral_restr	0.084	0.2	568
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	5038
X-RAY DIFFRACTION	r_gen_planes_other	0.013	0.02	958
X-RAY DIFFRACTION	r_nbd_refined	0.208	0.2	736
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.214	0.2	3534
X-RAY DIFFRACTION	r_nbtor_refined	0.177	0.2	2121
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.074	0.2	1910
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.166	0.2	257
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.215	0.2	24
X-RAY DIFFRACTION	r_nbd_other	0.243	0.2	55
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.185	0.2	23
X-RAY DIFFRACTION	r_mcbond_it	1.8	3.978	2112
X-RAY DIFFRACTION	r_mcbond_other	1.798	3.976	2111
X-RAY DIFFRACTION	r_mcangle_it	2.947	5.964	2640
X-RAY DIFFRACTION	r_mcangle_other	2.947	5.965	2641
X-RAY DIFFRACTION	r_scbond_it	2.535	4.323	2379
X-RAY DIFFRACTION	r_scbond_other	2.535	4.324	2380
X-RAY DIFFRACTION	r_scangle_it	4.098	6.349	3436
X-RAY DIFFRACTION	r_scangle_other	4.097	6.35	3437
X-RAY DIFFRACTION	r_lrange_it	5.926	45.819	4826
X-RAY DIFFRACTION	r_lrange_other	5.853	45.596	4766

LS refinement shell

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

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.2-2.257	0.26	156	0.229	3137	0.23	3310	0.899	0.907	99.4864	0.195
2.257-2.319	0.235	168	0.224	3053	0.225	3232	0.912	0.913	99.6597	0.194
2.319-2.386	0.209	157	0.217	2971	0.217	3137	0.927	0.927	99.7131	0.187
2.386-2.46	0.256	150	0.21	2864	0.213	3022	0.91	0.928	99.7353	0.181
2.46-2.54	0.274	145	0.206	2776	0.209	2929	0.904	0.926	99.7269	0.179
2.54-2.629	0.233	156	0.208	2700	0.209	2861	0.927	0.931	99.8252	0.181
2.629-2.728	0.2	131	0.206	2609	0.206	2743	0.949	0.942	99.8906	0.183
2.728-2.84	0.25	127	0.198	2520	0.2	2648	0.927	0.932	99.9622	0.179
2.84-2.966	0.249	132	0.193	2427	0.195	2560	0.919	0.934	99.9609	0.177
2.966-3.111	0.205	114	0.18	2326	0.181	2443	0.936	0.945	99.8772	0.171
3.111-3.279	0.232	133	0.187	2184	0.189	2317	0.935	0.944	100	0.182
3.279-3.477	0.18	92	0.18	2120	0.18	2212	0.96	0.958	100	0.182
3.477-3.717	0.209	112	0.189	1974	0.19	2088	0.948	0.952	99.9042	0.194
3.717-4.015	0.198	92	0.165	1837	0.166	1929	0.953	0.961	100	0.174
4.015-4.397	0.178	94	0.156	1697	0.158	1792	0.963	0.967	99.9442	0.173
4.397-4.915	0.159	86	0.149	1526	0.149	1613	0.973	0.971	99.938	0.173
4.915-5.673	0.203	73	0.175	1386	0.176	1459	0.958	0.965	100	0.197
5.673-6.943	0.208	73	0.212	1163	0.212	1237	0.949	0.947	99.9192	0.234
6.943-9.798	0.18	58	0.173	911	0.174	970	0.958	0.959	99.8969	0.202
9.798-104.676	0.256	24	0.219	556	0.221	583	0.892	0.927	99.4854	0.255

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