PDB-8qk8: Structure of Legionella pneumophila Lcl C-terminal domain bound t...

ID or keywords:

Entry

Database: PDB / ID: 8qk8

Title

Structure of Legionella pneumophila Lcl C-terminal domain bound to sulphate

Components

HbP1

Keywords

CELL ADHESION / Lcl / T2SS / adhesion / biofilm / Legionella pneumophila / collagen

Function / homology

Protein of unknown function DUF1566 / Lcl C-terminal domain / : / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / HbP1

Function and homology information

Biological species

Legionella pneumophila 130b (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

Rehman, S. / Garnett, J.A.

Funding support

United Kingdom, 2items

Citation

Journal: Biorxiv / Year: 2023
Title: The Legionella collagen-like protein employs a unique binding mechanism for the recognition of host glycosaminoglycans.
Authors: Rehman, S. / Antonovic, A.K. / McIntire, I.E. / Zheng, H. / Cleaver, L. / Adams, C.O. / Portlock, T. / Richardson, K. / Shaw, R. / Oregioni, A. / Mastroianni, G. / Whittaker, S.B. / Kelly, G. ...

History

Deposition	Sep 14, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 27, 2023	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8qk8.cif.gz	111.2 KB	Display	PDBx/mmCIF format
PDB format	pdb8qk8.ent.gz	85.6 KB	Display	PDB format
PDBx/mmJSON format	8qk8.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qk/8qk8 ftp://data.pdbj.org/pub/pdb/validation_reports/qk/8qk8	HTTPS FTP

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Related structure data

Related structure data	8q4eC C: citing same article (ref.)
Similar structure data	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	#4 - Apr 2000 Collagen similarity (1)

Deposited unit

A: HbP1

B: HbP1

hetero molecules

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

1

A: HbP1

hetero molecules

A: HbP1

hetero molecules

A: HbP1

hetero molecules

defined by author&software
Evidence: SAXS
56.3 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: HbP1

defined by author&software
Evidence: SAXS
55.7 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	74.910, 74.910, 94.970
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	150
Space group name H-M	P321

Components on special symmetry positions

ID	Model	Components
1	1	B-499- HOH

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: PHE / End label comp-ID: PHE / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 256 - 386 / Label seq-ID: 35 - 165

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

#1: Protein	HbP1 Mass: 18572.584 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Legionella pneumophila 130b (bacteria) / Gene: hbP1 / Production host: Escherichia coli (E. coli) / References: UniProt: E7BLH6
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄ / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 194 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	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: 2.07 Å³/Da / Density % sol: 40.6 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 20% (v/v) glycerol, 20% (w/v) polyethylene glycol (PEG) 4000, 30 mM NaNO3, 30 mM Na2HPO4, 30 mM (NH4)2SO4, 100 mM bicine, 100 mM tris-HCl

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 26, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97625 Å / Relative weight: 1
Reflection	Resolution: 1.9→64.91 Å / Num. obs: 24856 / % possible obs: 100 % / Redundancy: 19.3 % / B_iso Wilson estimate: 24.7 Å² / R_merge(I) obs: 0.074 / Net I/σ(I): 28.7
Reflection shell	Resolution: 1.9→1.93 Å / Redundancy: 14.8 % / R_merge(I) obs: 0.541 / Mean I/σ(I) obs: 5.8 / Num. unique obs: 1235 / % possible all: 99.8

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0415	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.9→64.874 Å / Cor.coef. F_o:F_c: 0.967 / Cor.coef. F_o:F_c free: 0.96 / WR_factor R_free: 0.184 / WR_factor R_work: 0.161 / Average fsc free: 0.9754 / Average fsc work: 0.9835 / Cross valid method: FREE R-VALUE / ESU R: 0.122 / ESU R Free: 0.112
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1874	1200	4.828 %
R_work	0.1604	23654	-
all	0.162	-	-
obs	-	24854	99.968 %

Solvent computation

Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 25.968 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.222 Å²	0.111 Å²	0 Å²
2-	-	0.222 Å²	0 Å²
3-	-	-	-0.721 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→64.874 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2058	0	10	194	2262

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.011	2112
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.016	1940
X-RAY DIFFRACTION	r_angle_refined_deg	1.462	1.639	2868
X-RAY DIFFRACTION	r_angle_other_deg	0.761	1.589	4434
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.799	5	260
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	5.635	5	14
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.454	10	338
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	16.377	10	104
X-RAY DIFFRACTION	r_chiral_restr	0.065	0.2	308
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	2602
X-RAY DIFFRACTION	r_gen_planes_other	0.01	0.02	538
X-RAY DIFFRACTION	r_nbd_refined	0.198	0.2	399
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.205	0.2	1798
X-RAY DIFFRACTION	r_nbtor_refined	0.18	0.2	1036
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.085	0.2	1160
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.165	0.2	156
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.168	0.2	12
X-RAY DIFFRACTION	r_nbd_other	0.232	0.2	73
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.158	0.2	19
X-RAY DIFFRACTION	r_mcbond_it	2.227	2.547	1046
X-RAY DIFFRACTION	r_mcbond_other	2.226	2.546	1046
X-RAY DIFFRACTION	r_mcangle_it	3.138	4.56	1304
X-RAY DIFFRACTION	r_mcangle_other	3.138	4.559	1305
X-RAY DIFFRACTION	r_scbond_it	3.831	2.915	1066
X-RAY DIFFRACTION	r_scbond_other	3.811	2.909	1059
X-RAY DIFFRACTION	r_scangle_it	5.743	5.144	1564
X-RAY DIFFRACTION	r_scangle_other	5.714	5.134	1553
X-RAY DIFFRACTION	r_lrange_it	6.791	26.182	2444
X-RAY DIFFRACTION	r_lrange_other	6.726	24.995	2400
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.073	0.05	4358

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.07251	0.05009
1	2	A	X-RAY DIFFRACTION	Local ncs	0.07251	0.05009

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
1.9-1.949	0.249	93	0.188	1733	0.191	1829	0.963	0.977	99.836	0.158
1.949-2.003	0.195	72	0.175	1673	0.176	1745	0.968	0.981	100	0.148
2.003-2.061	0.199	56	0.159	1666	0.16	1722	0.979	0.984	100	0.137
2.061-2.124	0.236	79	0.164	1584	0.167	1663	0.968	0.983	100	0.14
2.124-2.194	0.214	100	0.162	1532	0.165	1632	0.972	0.984	100	0.142
2.194-2.271	0.252	64	0.165	1493	0.168	1557	0.961	0.984	100	0.147
2.271-2.356	0.212	89	0.161	1398	0.164	1488	0.971	0.985	99.9328	0.144
2.356-2.452	0.19	79	0.166	1396	0.167	1475	0.98	0.984	100	0.15
2.452-2.561	0.175	76	0.169	1330	0.17	1406	0.98	0.983	100	0.155
2.561-2.686	0.166	59	0.16	1290	0.16	1350	0.985	0.984	99.9259	0.146
2.686-2.831	0.223	56	0.162	1213	0.164	1269	0.974	0.984	100	0.153
2.831-3.002	0.162	64	0.155	1158	0.155	1222	0.982	0.986	100	0.152
3.002-3.209	0.229	38	0.161	1106	0.163	1144	0.972	0.984	100	0.162
3.209-3.466	0.165	52	0.167	1018	0.167	1070	0.983	0.983	100	0.171
3.466-3.795	0.227	58	0.151	939	0.155	997	0.976	0.987	100	0.16
3.795-4.242	0.164	57	0.146	838	0.147	896	0.984	0.986	99.8884	0.161
4.242-4.894	0.122	37	0.137	772	0.136	809	0.993	0.99	100	0.157
4.894-5.986	0.142	39	0.17	654	0.168	693	0.989	0.987	100	0.195
5.986-8.429	0.213	25	0.171	530	0.173	555	0.979	0.982	100	0.195
8.429-64.874	0.135	7	0.178	330	0.177	338	0.971	0.972	99.7041	0.223

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