PDB-6qvi: Crystal structure of competence-associated pilin ComZ from Thermu...

ID or keywords:

Entry

Database: PDB / ID: 6qvi

Title

Crystal structure of competence-associated pilin ComZ from Thermus thermophilus

Components

ComZ

Keywords

DNA BINDING PROTEIN / competence pilin / DNA receptor / beta-solenoid domain / pseudopilin-like domain

Function / homology

membrane => GO:0016020 / ComZ

Function and homology information

Biological species

Thermus thermophilus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.72 Å

Authors

Karuppiah, V. / Derrick, J.P.

Funding support

United Kingdom, 1items

Citation

Journal: Mbio / Year: 2019
Title: Structure and Properties of a Natural Competence-Associated Pilin Suggest a Unique Pilus Tip-Associated DNA Receptor.
Authors: Salleh, M.Z. / Karuppiah, V. / Snee, M. / Thistlethwaite, A. / Levy, C.W. / Knight, D. / Derrick, J.P.

History

Deposition	Mar 1, 2019	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 29, 2019	Provider: repository / Type: Initial release
Revision 1.1	Jun 26, 2019	Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Aug 21, 2019	Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6qvi.cif.gz	588.4 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qv/6qvi ftp://data.pdbj.org/pub/pdb/validation_reports/qv/6qvi	HTTPS FTP

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Related structure data

Related structure data	6qvfC C: citing same article (ref.)
Similar structure data	5ho9-1 6cvs-d 5do9-6 1n4l-d 66 3p20-d 1jva-1 5ho9-2 Search similar-shape structures by Omokage search (details) 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 - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

6qvfC

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: ComZ

B: ComZ

C: ComZ

172 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: ComZ

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

2

B: ComZ

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

3

C: ComZ

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

Unit cell

Length a, b, c (Å)	121.860, 121.860, 212.350
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	152
Space group name H-M	P3₁21

#1: Protein	ComZ Mass: 57485.031 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria) Strain: HB27 / ATCC BAA-163 / DSM 7039 / Gene: comZ, TT_C0857 / Production host: Escherichia coli (E. coli) / References: UniProt: Q72JC1
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal	Density Matthews: 2.64 Å³/Da / Density % sol: 53.4 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 0.2 M potassium thiocyanate, 0.1 M Bis-Tris propane pH 6.5 and 20% w/v PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 2, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.72→58.79 Å / Num. obs: 49699 / % possible obs: 99.9 % / Redundancy: 5.8 % / B_iso Wilson estimate: 73.87 Å² / R_merge(I) obs: 0.058 / Net I/σ(I): 18.1
Reflection shell	Resolution: 2.72→2.79 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 2 / % possible all: 99.9

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Processing

Software

Name	Classification
XDS	data reduction
XSCALE	data scaling
AutoSol	phasing
PHENIX	refinement

Refinement

Method to determine structure:

SAD / Resolution: 2.72→58.79 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30

	R_factor	Num. reflection	% reflection
R_free	0.267	2514	5.07 %
R_work	0.206	-	-
obs	0.209	49626	99.8 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 2.72→58.79 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11505	0	0	15	11520

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.012	11845
X-RAY DIFFRACTION	f_angle_d	1.551	16081
X-RAY DIFFRACTION	f_dihedral_angle_d	8.408	7012
X-RAY DIFFRACTION	f_chiral_restr	0.083	1794
X-RAY DIFFRACTION	f_plane_restr	0.009	2136

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.7201-2.7724	0.4357	134	0.3615	2586	X-RAY DIFFRACTION	100
2.7724-2.829	0.3816	137	0.3359	2584	X-RAY DIFFRACTION	100
2.829-2.8905	0.3723	143	0.3012	2561	X-RAY DIFFRACTION	100
2.8905-2.9577	0.3411	132	0.2848	2583	X-RAY DIFFRACTION	100
2.9577-3.0317	0.343	130	0.2643	2603	X-RAY DIFFRACTION	100
3.0317-3.1136	0.3322	155	0.2594	2578	X-RAY DIFFRACTION	100
3.1136-3.2053	0.3235	146	0.2424	2582	X-RAY DIFFRACTION	100
3.2053-3.3087	0.316	143	0.2361	2583	X-RAY DIFFRACTION	100
3.3087-3.427	0.2953	108	0.2284	2616	X-RAY DIFFRACTION	100
3.427-3.5641	0.2675	147	0.2183	2600	X-RAY DIFFRACTION	100
3.5641-3.7263	0.2901	111	0.2082	2625	X-RAY DIFFRACTION	100
3.7263-3.9228	0.2654	147	0.2081	2618	X-RAY DIFFRACTION	100
3.9228-4.1685	0.2667	153	0.1856	2598	X-RAY DIFFRACTION	100
4.1685-4.4902	0.2643	153	0.1765	2633	X-RAY DIFFRACTION	100
4.4902-4.9419	0.2207	155	0.1468	2613	X-RAY DIFFRACTION	100
4.9419-5.6565	0.2242	154	0.1752	2648	X-RAY DIFFRACTION	100
5.6565-7.1246	0.2694	151	0.2163	2661	X-RAY DIFFRACTION	100
7.1246-58.7989	0.2352	115	0.2011	2840	X-RAY DIFFRACTION	99

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	5.6301	1.1101	2.3539	2.1906	0.7096	3.1802	0.0382	0.4189	-0.044	0.2405	0.003	0.0874	1.0104	0.2966	-0.0041	0.8527	0.1169	0.0721	0.2628	-0.0112	0.4169	39.5948	31.4745	120.3695
2	6.3841	0.3175	-2.2167	2.0827	0.9541	2.4168	-0.4295	0.5978	-0.8206	0.2978	-0.0488	0.0719	0.4448	-0.3045	0.3928	0.4392	-0.1006	0.119	0.7489	-0.0576	0.472	43.1005	30.5556	77.5772
3	0.403	0.5214	0.9486	1.4025	2.3168	3.1604	-0.3436	0.265	-0.0049	0.0297	-0.2803	0.1703	0.4542	-0.3259	0.7315	0.4464	0.0032	0.0205	0.6081	0.0794	0.4773	42.7151	33.7461	101.9074
4	2.3017	0.8787	-0.3687	2.6773	-0.6685	5.7146	0.1974	-0.1373	-0.21	0.1633	-0.2126	0.6771	0.0254	-0.6289	-0.0618	0.4125	-0.1802	-0.048	0.5451	-0.0334	0.7023	48.9361	14.113	-6.8009
5	2.292	0.9021	0.6032	3.9064	1.0066	1.9602	-0.1939	-0.03	-0.4618	-0.0196	0.1115	0.1898	0.643	-0.7109	0.1093	0.895	-0.472	0.1957	1.2183	-0.0765	0.6442	52.6437	16.9047	34.5779
6	0.7017	0.0094	-1.7987	0.4014	-1.0943	5.4373	-0.1352	-0.258	-0.4423	0.4105	-0.3059	0.1798	0.7079	-0.4237	0.3301	0.8596	-0.4283	0.1226	0.866	0.0663	0.8488	53.2439	13.2389	20.1975
7	1.4747	-0.6571	-0.3738	0.3173	-0.423	2.3878	0.4432	-0.1423	-0.087	0.2539	-0.0045	0.3841	-0.4788	0.0182	-0.2962	1.3181	-0.3055	0.2041	0.5179	-0.0563	0.7311	-3.0213	22.1317	98.0803
8	2.2323	0.6619	-0.1595	7.2017	-0.0101	3.9238	0.007	-0.1803	0.434	-0.4435	-0.2965	0.6565	0.2351	0.4125	0.332	0.6416	0.3194	-0.236	0.7601	-0.2765	0.7952	-3.0599	20.0061	56.5566
9	1.2549	0.2409	2.4531	0.4837	-1.1343	5.7543	0.1856	-0.189	0.2097	0.5415	-0.7305	0.2277	-0.1061	-0.2386	0.4568	1.1693	-0.0977	0.099	0.7679	-0.2739	0.648	-0.4997	19.1031	81.1191

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'A' AND (RESID 1 THROUGH 128 )
2	X-RAY DIFFRACTION	2	CHAIN 'A' AND (RESID 129 THROUGH 488 )
3	X-RAY DIFFRACTION	3	CHAIN 'A' AND (RESID 489 THROUGH 528 )
4	X-RAY DIFFRACTION	4	CHAIN 'B' AND (RESID 1 THROUGH 139 )
5	X-RAY DIFFRACTION	5	CHAIN 'B' AND (RESID 140 THROUGH 476 )
6	X-RAY DIFFRACTION	6	CHAIN 'B' AND (RESID 477 THROUGH 526 )
7	X-RAY DIFFRACTION	7	CHAIN 'C' AND (RESID 1 THROUGH 139 )
8	X-RAY DIFFRACTION	8	CHAIN 'C' AND (RESID 140 THROUGH 489 )
9	X-RAY DIFFRACTION	9	CHAIN 'C' AND (RESID 490 THROUGH 527 )

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