PDB-4uqw: Coevolution of the ATPase ClpV, the TssB-TssC Sheath and the Acce...

ID or keywords:

Entry

Database: PDB / ID: 4uqw

Title

Coevolution of the ATPase ClpV, the TssB-TssC Sheath and the Accessory HsiE Protein Distinguishes Two Type VI Secretion Classes

Components

PROTEIN CLPV1

Keywords

CHAPERONE / SECRETION / SHEATH / DISASSEMBLY / REGULATION / BACTERIAL

Function / homology

Function and homology information

ATP hydrolysis activity / ATP binding / cytoplasm
Similarity search - Function

Biological species

PSEUDOMONAS AERUGINOSA PAO1 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.5 Å

Authors

Forster, A. / Planamente, S. / Manoli, E. / Lossi, N.S. / Freemont, P.S. / Filloux, A.

Citation

Journal: J.Biol.Chem. / Year: 2014
Title: Coevolution of the ATPase Clpv, the Sheath Proteins Tssb and Tssc and the Accessory Protein Tagj/Hsie1 Distinguishes Type Vi Secretion Classes.
Authors: Forster, A. / Planamente, S. / Manoli, E. / Lossi, N.S. / Freemont, P.S. / Filloux, A.

History

Deposition	Jun 25, 2014	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 22, 2014	Provider: repository / Type: Initial release
Revision 1.1	Dec 10, 2014	Group: Database references
Revision 1.2	Jan 10, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4uqw.cif.gz	148.1 KB	Display	PDBx/mmCIF format
PDB format	pdb4uqw.ent.gz	118.9 KB	Display	PDB format
PDBx/mmJSON format	4uqw.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4uqw_validation.pdf.gz	443.5 KB	Display	wwPDB validaton report
Full document	4uqw_full_validation.pdf.gz	444.4 KB	Display
Data in XML	4uqw_validation.xml.gz	17.8 KB	Display
Data in CIF	4uqw_validation.cif.gz	26.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/uq/4uqw ftp://data.pdbj.org/pub/pdb/validation_reports/uq/4uqw	HTTPS FTP

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Related structure data

Related structure data	4uqxC 4uqyC 4uqzC 3zrjS 4uqn PDB Unreleased entry C: citing same article (ref.) S: Starting model for refinement
Similar structure data	3u04-d 4hh5-d 3s0t-1 6pbs-3 6pbs-7 1qhy-d 3sdw-d 5u2u-2 6pbs-1 4h2d-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 - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#32 - Aug 2002 Chaperones similarity (1) #80 - Aug 2006 AAA+ Proteases similarity (4) #176 - Aug 2014 Dynein similarity (4) #220 - Apr 2018 Dehalogenases similarity (1) #150 - Jun 2012 Sliding Clamps similarity (1)

Deposited unit

A: PROTEIN CLPV1

B: PROTEIN CLPV1

hetero molecules

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

1

A: PROTEIN CLPV1

hetero molecules

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

2

B: PROTEIN CLPV1

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

Unit cell

Length a, b, c (Å)	90.530, 90.530, 54.310
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	76
Space group name H-M	P4₁

Noncrystallographic symmetry (NCS)

NCS oper: (Code: given
Matrix: (0.4876, -0.5142, 0.7056), (-0.8643, -0.3988, 0.3066), (0.1237, -0.7593, -0.6388)
Vector: 57.5493, 129.2628, 58.6101)

#1: Protein	PROTEIN CLPV1 / CLPV Mass: 18075.559 Da / Num. of mol.: 2 / Fragment: N DOMAIN, RESIDUES 1-161 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PSEUDOMONAS AERUGINOSA PAO1 (bacteria) / Production host: ESCHERICHIA COLI B (bacteria) / Strain (production host): B834 / References: UniProt: Q9I742
#2: Chemical	ChemComp-BEN / BENZAMIDINE Mass: 120.152 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₇H₈N₂
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 358 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.09 Å³/Da / Density % sol: 60.2 % / Description: NONE
Crystal grow	pH: 8 / Details: 0.2 M SODIUM MALONATE 20% PEG 3350, PH 8.0

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 20, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.5→90.5 Å / Num. obs: 70465 / % possible obs: 99.9 % / Observed criterion σ(I): 1.5 / Redundancy: 4.6 % / B_iso Wilson estimate: 19.05 Å² / R_merge(I) obs: 0.08 / Net I/σ(I): 8.8
Reflection shell	Resolution: 1.5→1.53 Å / Redundancy: 4.7 % / R_merge(I) obs: 0.71 / Mean I/σ(I) obs: 1.9 / % possible all: 99.9

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZRJ

3zrj

Resolution: 1.5→46.572 Å / SU ML: 0.16 / σ(F): 1.36 / Phase error: 17.73 / Stereochemistry target values: ML / Details: RESIDUES 82-84 IN CHAIN A ARE DISORDERED

	R_factor	Num. reflection	% reflection
R_free	0.1814	3555	5.1 %
R_work	0.1593	-	-
obs	0.1604	70443	99.93 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 28.25 Å²

Refinement step

Cycle: LAST / Resolution: 1.5→46.572 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2505	0	9	358	2872

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.016	2636
X-RAY DIFFRACTION	f_angle_d	1.645	3589
X-RAY DIFFRACTION	f_dihedral_angle_d	14.134	982
X-RAY DIFFRACTION	f_chiral_restr	0.091	410
X-RAY DIFFRACTION	f_plane_restr	0.009	462

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 (%)
1.5-1.5205	0.2561	165	0.2451	2639	X-RAY DIFFRACTION	100
1.5205-1.5423	0.2704	124	0.2435	2666	X-RAY DIFFRACTION	100
1.5423-1.5653	0.2222	141	0.2358	2683	X-RAY DIFFRACTION	100
1.5653-1.5897	0.2585	125	0.238	2658	X-RAY DIFFRACTION	100
1.5897-1.6158	0.2739	140	0.2221	2658	X-RAY DIFFRACTION	100
1.6158-1.6437	0.2593	126	0.2089	2706	X-RAY DIFFRACTION	100
1.6437-1.6736	0.2368	123	0.2074	2650	X-RAY DIFFRACTION	100
1.6736-1.7057	0.2084	147	0.1973	2687	X-RAY DIFFRACTION	100
1.7057-1.7406	0.2394	132	0.1813	2649	X-RAY DIFFRACTION	100
1.7406-1.7784	0.1909	161	0.1755	2647	X-RAY DIFFRACTION	100
1.7784-1.8198	0.2031	139	0.1701	2660	X-RAY DIFFRACTION	100
1.8198-1.8653	0.2205	143	0.1677	2640	X-RAY DIFFRACTION	100
1.8653-1.9157	0.1944	147	0.1667	2692	X-RAY DIFFRACTION	100
1.9157-1.9721	0.1727	143	0.1578	2655	X-RAY DIFFRACTION	100
1.9721-2.0358	0.1726	141	0.1559	2666	X-RAY DIFFRACTION	100
2.0358-2.1085	0.1664	133	0.1544	2714	X-RAY DIFFRACTION	100
2.1085-2.1929	0.1841	142	0.1422	2636	X-RAY DIFFRACTION	100
2.1929-2.2927	0.1711	143	0.1385	2681	X-RAY DIFFRACTION	100
2.2927-2.4136	0.1799	151	0.1491	2665	X-RAY DIFFRACTION	100
2.4136-2.5648	0.1839	145	0.1563	2680	X-RAY DIFFRACTION	100
2.5648-2.7628	0.1815	149	0.1562	2690	X-RAY DIFFRACTION	100
2.7628-3.0408	0.1808	143	0.1621	2690	X-RAY DIFFRACTION	100
3.0408-3.4807	0.1788	152	0.1528	2696	X-RAY DIFFRACTION	100
3.4807-4.3848	0.1622	144	0.1385	2703	X-RAY DIFFRACTION	100
4.3848-46.5947	0.15	156	0.1485	2777	X-RAY DIFFRACTION	100

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	0.174	0.082	-0.0846	0.6056	0.0677	0.0748	-0.1632	-1.0134	-0.0871	0.805	-0.3549	-0.1507	0.8911	-0.761	-0.0217	0.3808	-0.0526	-0.0044	0.4099	-0.0138	0.1934	23.7038	85.3771	20.2217
2	0.0043	0.0488	-0.0519	0.0673	0.0128	0.0434	0.0578	0.1316	-0.0708	-0.1056	-0.0669	-0.0259	0.0273	0.114	0.0001	0.1195	-0.0005	0.0054	0.1597	-0.0074	0.1585	25.8844	85.9397	6.8829
3	0.1964	-0.1532	-0.1976	0.1182	0.0558	0.5902	0.0292	0.306	-0.587	-0.1414	0.0424	0.2013	0.0788	0.1636	-0.002	0.1804	0.0026	-0.003	0.215	-0.0446	0.2091	35.3852	78.9584	-0.0842
4	0.0951	0.1923	-0.0413	0.3099	-0.1027	0.0303	0.0168	0.0877	-0.0868	-0.0104	-0.0583	-0.125	-0.0181	0.1548	0	0.1432	0.0283	0.0077	0.1992	-0.0094	0.1674	40.5718	83.8657	0.7212
5	0.1169	0.1706	0.0435	0.1453	0.0554	0.2871	0.0865	0.3757	0.0329	-0.2427	-0.0335	-0.0406	-0.0073	-0.0195	0	0.1974	0.0257	0.022	0.2564	0.003	0.1525	36.9644	94.9159	-11.2602
6	0.6318	0.328	0.1442	1.1992	0.3688	1.2368	-0.1075	-0.123	-0.3372	-0.0285	-0.2423	-0.2366	0.0364	0.4865	-0.4678	0.1686	0.013	0.0544	0.3251	0.0422	0.2245	49.7283	88.0124	-5.3939
7	2.1781	-0.2319	-0.0372	1.4647	0.8557	0.6318	-0.1815	-0.7301	-0.5341	0.674	-0.3342	-0.6505	0.4783	0.6629	-0.7587	0.1736	0.1004	0.0151	0.3247	0.1763	0.3662	44.293	76.9972	9.4648
8	0.6859	0.209	-0.4536	0.7226	0.2189	0.6904	0.0348	-0.0279	0.1473	0.0734	-0.013	0.0981	-0.1503	-0.0511	0	0.1479	0.0069	0.0056	0.1687	-0.0112	0.1478	29.2023	96.1153	4.2556
9	0.0393	-0.0045	-0.0563	0.0507	-0.034	0.0332	0.1435	-0.4413	0.3652	-0.1331	0.0421	-0.4965	-0.44	0.5746	-0.0003	0.2069	-0.025	-0.0028	0.3013	-0.04	0.233	43.9166	97.1331	5.4471
10	0.065	0.0581	-0.1412	0.1165	-0.0378	0.2683	-0.0192	-0.0277	0.367	-0.1066	0.0773	-0.1252	-0.2644	0.1422	-0.0001	0.233	-0.0016	0.0265	0.2204	0.0107	0.2172	39.123	103.1394	-3.5365
11	0.1157	-0.033	-0.125	0.0304	-0.0143	0.1772	0.0953	0.3155	0.1427	-0.0237	0.1004	0.1127	-0.024	-0.0955	0.001	0.1918	0.032	-0.0075	0.2643	0.0433	0.1541	28.5527	98.8981	-10.2394
12	0.2191	-0.0697	-0.1985	0.2506	-0.1593	1.088	-0.1309	0.3209	-0.2779	-0.2063	0.456	-0.5768	-0.0189	0.806	-0.025	0.1877	0.0037	0.038	0.3573	-0.124	0.2869	17.4378	69.6359	-4.4932
13	0.5374	0.6497	-0.0888	0.5428	-0.1093	-0.045	0.0197	0.1036	-0.0089	-0.0603	-0.0732	-0.2608	0.0065	-0.0095	0.0001	0.1822	-0.0039	0.0177	0.1491	-0.0003	0.215	25.4888	75.9894	6.5254
14	0.7017	0.8202	-0.196	0.8474	0.1154	0.2179	0.0774	-0.1406	-0.2033	0.0657	-0.1244	-0.3013	-0.005	-0.0997	-0.0241	0.142	0.0027	-0.0065	0.1479	0.0099	0.227	22.3296	72.7926	11.741
15	0.6043	-0.082	0.6229	0.0982	0.017	0.5687	0.0881	-0.6	0.5243	0.4005	-0.1654	0.2042	-0.0185	-0.6636	-0.1218	0.2403	-0.0757	0.029	0.3362	-0.0284	0.1423	9.7425	76.3268	20.9334
16	0.6497	0.3926	-0.4399	0.9559	0.0204	0.3143	-0.0189	-0.2186	-0.3998	0.3895	-0.2183	-0.5247	0.4984	0.4117	-0.0183	0.2922	0.0177	-0.0458	0.2857	0.0804	0.4032	26.5792	67.4258	16.2061
17	0.9146	0.5976	0.2879	0.1547	-0.0598	0.8313	0.0177	-0.0058	-0.2021	-0.0163	0.0303	0.0233	0.0887	-0.0675	0.0042	0.175	-0.0117	-0.0267	0.1424	-0.0089	0.174	8.772	68.9992	4.3934
18	0.2792	-0.0999	-0.1866	0.0839	-0.1874	0.3599	0.1639	-0.1908	-0.4497	-0.1225	0.0618	0.2511	0.2922	-0.1323	0.0046	0.4444	-0.0606	-0.0031	0.2454	0.0367	0.3489	11.9281	62.5754	16.759
19	0.4813	0.0185	0.2397	0.2719	0.1629	0.3488	0.1561	-0.381	0.3584	0.1769	-0.1341	0.4709	0.0299	-0.3907	-0.0097	0.1874	-0.0474	0.0358	0.2807	-0.0126	0.2441	2.2286	75.4979	14.3349

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'A' AND (RESID -1 THROUGH 5 )
2	X-RAY DIFFRACTION	2	CHAIN 'A' AND (RESID 6 THROUGH 14 )
3	X-RAY DIFFRACTION	3	CHAIN 'A' AND (RESID 15 THROUGH 31 )
4	X-RAY DIFFRACTION	4	CHAIN 'A' AND (RESID 32 THROUGH 47 )
5	X-RAY DIFFRACTION	5	CHAIN 'A' AND (RESID 48 THROUGH 63 )
6	X-RAY DIFFRACTION	6	CHAIN 'A' AND (RESID 64 THROUGH 77 )
7	X-RAY DIFFRACTION	7	CHAIN 'A' AND (RESID 78 THROUGH 89 )
8	X-RAY DIFFRACTION	8	CHAIN 'A' AND (RESID 90 THROUGH 124 )
9	X-RAY DIFFRACTION	9	CHAIN 'A' AND (RESID 125 THROUGH 134 )
10	X-RAY DIFFRACTION	10	CHAIN 'A' AND (RESID 135 THROUGH 148 )
11	X-RAY DIFFRACTION	11	CHAIN 'A' AND (RESID 149 THROUGH 160 )
12	X-RAY DIFFRACTION	12	CHAIN 'B' AND (RESID 1 THROUGH 14 )
13	X-RAY DIFFRACTION	13	CHAIN 'B' AND (RESID 15 THROUGH 31 )
14	X-RAY DIFFRACTION	14	CHAIN 'B' AND (RESID 32 THROUGH 51 )
15	X-RAY DIFFRACTION	15	CHAIN 'B' AND (RESID 52 THROUGH 63 )
16	X-RAY DIFFRACTION	16	CHAIN 'B' AND (RESID 64 THROUGH 89 )
17	X-RAY DIFFRACTION	17	CHAIN 'B' AND (RESID 90 THROUGH 122 )
18	X-RAY DIFFRACTION	18	CHAIN 'B' AND (RESID 123 THROUGH 142 )
19	X-RAY DIFFRACTION	19	CHAIN 'B' AND (RESID 143 THROUGH 160 )

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