PDB-3jvu: Crystal structure of unliganded P. aeruginosa PilT

ID or keywords:

Entry

Database: PDB / ID: 3jvu

Title

Crystal structure of unliganded P. aeruginosa PilT

Components

Twitching mobility protein

Keywords

ATP binding protein / Motor protein / P-loop atpase / type iv pili / ATP-binding / Fimbrium / Nucleotide-binding / Transport

Function / homology

Function and homology information

pilus retraction / type IV pilus / type IV pilus-dependent motility / ATP hydrolysis activity / ATP binding / cytoplasm
Similarity search - Function

Biological species

Pseudomonas aeruginosa (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.1 Å

Authors

Misic, A.M. / Satyshur, K.A. / Forest, K.T.

Citation

Journal: J.Mol.Biol. / Year: 2010
Title: P. aeruginosa PilT structures with and without nucleotide reveal a dynamic type IV pilus retraction motor.
Authors: Misic, A.M. / Satyshur, K.A. / Forest, K.T.

History

Deposition	Sep 17, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 21, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Sep 6, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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	3jvu.cif.gz	201.5 KB	Display	PDBx/mmCIF format
PDB format	pdb3jvu.ent.gz	162.3 KB	Display	PDB format
PDBx/mmJSON format	3jvu.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3jvu_validation.pdf.gz	481.9 KB	Display	wwPDB validaton report
Full document	3jvu_full_validation.pdf.gz	556.6 KB	Display
Data in XML	3jvu_validation.xml.gz	46.9 KB	Display
Data in CIF	3jvu_validation.cif.gz	62.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/jv/3jvu ftp://data.pdbj.org/pub/pdb/validation_reports/jv/3jvu	HTTPS FTP

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Related structure data

Related structure data	3jvvC 2ewvS 2eww 2gsz C: citing same article (ref.) S: Starting model for refinement
Similar structure data	3jvv-1 6ojy-d 6ok2-d 6okv-d 6oll-d 6ojz-d 6olk-d 2xsz-d 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	#211 - Jul 2017 Pilus Machine similarity (3)

Deposited unit

A: Twitching mobility protein

B: Twitching mobility protein

C: Twitching mobility protein

hetero molecules

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

1

A: Twitching mobility protein

B: Twitching mobility protein

C: Twitching mobility protein

hetero molecules

A: Twitching mobility protein

B: Twitching mobility protein

C: Twitching mobility protein

hetero molecules

defined by author&software
237 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	108.240, 121.378, 184.406
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	1	A	1 - 81
2	1	1	1	B	1 - 81
3	1	1	1	C	1 - 81
1	1	2	1	A	83 - 103
2	1	2	1	B	83 - 103
3	1	2	1	C	83 - 103
1	1	3	1	A	108 - 130
2	1	3	1	B	108 - 130
3	1	3	1	C	108 - 130
1	1	4	1	A	140 - 155
2	1	4	1	B	140 - 155
3	1	4	1	C	140 - 155
1	1	5	1	A	165 - 200
2	1	5	1	B	165 - 200
3	1	5	1	C	165 - 200
1	1	6	1	A	210 - 220
2	1	6	1	B	210 - 220
3	1	6	1	C	210 - 220
1	1	7	1	A	230 - 343
2	1	7	1	B	230 - 343
3	1	7	1	C	230 - 343

NCS ensembles :

ID
1
2
3
4
5
6
7

#1: Protein	Twitching mobility protein Mass: 39414.328 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PA103 / Gene: PA0395, pilT / Plasmid: pET-23a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P24559
#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical	ChemComp-CIT / CITRIC ACID Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₈O₇
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.56 Å³/Da / Density % sol: 51.97 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Mother liquor: 100 mM Hepes, 8% PEG 6000, Protein buffer contains MES, NaCl, glycerol, citrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.979 Å
Detector	Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Aug 5, 2007 / Details: mirrors
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 3.1→30 Å / Num. all: 20179 / Num. obs: 20179 / % possible obs: 94.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / B_iso Wilson estimate: 59.8 Å² / R_sym value: 0.098 / Net I/σ(I): 17.3
Reflection shell	Resolution: 3.1→3.21 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 3 / Num. unique all: 1652 / R_sym value: 0.384 / % possible all: 76.1

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Processing

Software

Name	Version	Classification
HKL-2000		data collection
PHASER		phasing
REFMAC	5.4.0067	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2EWV

2ewv

Resolution: 3.1→23.34 Å / Cor.coef. F_o:F_c: 0.917 / Cor.coef. F_o:F_c free: 0.856 / SU B: 53.387 / SU ML: 0.42 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.559 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: Anisotropic B values from TLS matrix

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.28195	1082	5.1 %	RANDOM
R_work	0.22905	-	-	-
obs	0.23165	20121	94.88 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 63.578 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-5.15 Å²	0 Å²	0 Å²
2-	-	11.43 Å²	0 Å²
3-	-	-	-6.29 Å²

Refinement step

Cycle: LAST / Resolution: 3.1→23.34 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7667	0	15	4	7686

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.022	7789
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.477	1.977	10502
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.364	5	979
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.245	23.68	337
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.406	15	1442
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.211	15	66
X-RAY DIFFRACTION	r_chiral_restr	0.07	0.2	1232
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.021	5719
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.83	2	4902
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.489	3	7917
X-RAY DIFFRACTION	r_scbond_it	0.879	2	2887
X-RAY DIFFRACTION	r_scangle_it	1.49	3	2585
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	650	tight positional	0.11	0.05
1	2	B	650	tight positional	0.09	0.05
1	3	C	650	tight positional	0.12	0.05
2	1	A	158	tight positional	0.12	0.05
2	2	B	158	tight positional	0.1	0.05
2	3	C	158	tight positional	0.08	0.05
3	1	A	171	tight positional	0.06	0.05
3	2	B	171	tight positional	0.11	0.05
3	3	C	171	tight positional	0.06	0.05
4	1	A	134	tight positional	0.05	0.05
4	2	B	134	tight positional	0.05	0.05
4	3	C	134	tight positional	0.05	0.05
5	1	A	291	tight positional	0.12	0.05
5	2	B	291	tight positional	0.07	0.05
5	3	C	291	tight positional	0.08	0.05
6	1	A	80	tight positional	0.04	0.05
6	2	B	80	tight positional	0.04	0.05
6	3	C	80	tight positional	0.04	0.05
7	1	A	637	tight positional	0.08	0.05
7	2	B	637	tight positional	0.11	0.05
7	3	C	637	tight positional	0.12	0.05
1	1	A	650	tight thermal	11.18	20
1	1	B	650	tight thermal	4.97	20
1	1	C	650	tight thermal	6.97	20
2	2	A	158	tight thermal	11.81	20
2	2	B	158	tight thermal	6.6	20
2	2	C	158	tight thermal	6.17	20
3	3	A	171	tight thermal	6.95	20
3	3	B	171	tight thermal	4.28	20
3	3	C	171	tight thermal	10.37	20
4	1	A	134	tight thermal	5.46	20
4	2	B	134	tight thermal	3.46	20
4	3	C	134	tight thermal	7.97	20
5	1	A	291	tight thermal	6.79	20
5	2	B	291	tight thermal	2.91	20
5	3	C	291	tight thermal	9.23	20
6	1	A	80	tight thermal	9.11	20
6	2	B	80	tight thermal	7.36	20
6	3	C	80	tight thermal	16.25	20
7	1	A	637	tight thermal	13.25	20
7	2	B	637	tight thermal	3.83	20
7	3	C	637	tight thermal	11.59	20

LS refinement shell

Resolution: 3.1→3.264 Å / Total num. of bins used: 10

	R_factor	Num. reflection	% reflection
R_free	0.442	114	-
R_work	0.331	2376	-
obs	-	-	78.52 %

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	7.6742	-1.1719	-0.1756	2.7529	1.35	10.9217	-0.1622	0.6908	0.6752	-0.3577	0.3346	0.3547	-0.9184	-0.4991	-0.1723	0.251	0.0165	-0.0554	0.3312	0.1632	0.3239	-13.938	39.822	37.653
2	0.1491	0.1497	0.0222	1.1866	0.8606	0.8221	-0.1464	-0.166	-0.1135	-0.2799	0.2538	-0.351	-0.2645	0.4882	-0.1075	0.2892	-0.0418	-0.0454	0.5536	0.1098	0.4686	-15.247	27.851	25.166
3	2.246	-0.2824	0.1301	4.0782	-1.961	3.0592	0.0382	-0.3829	0.0267	0.4423	0.1015	0.1517	0.0471	-0.0765	-0.1397	0.2965	-0.0113	0.0185	0.0855	-0.075	0.2912	-31.901	21.027	24.185
4	0.9125	-1.4011	0.1296	7.8622	-1.073	5.0595	-0.0743	-0.4392	-0.2247	0.2325	0.37	-0.3847	0.2743	0.2512	-0.2956	0.532	0.0421	-0.0004	0.3024	0.0138	0.3844	-22.458	3.293	29.158
5	5.4549	0.5729	-0.4716	1.6777	-0.1258	2.3632	0.0381	0.0835	0.8613	0.1049	0.0745	0.3997	-0.6242	-0.4407	-0.1127	0.5093	0.1051	0.0436	0.0846	0.0236	0.4255	-39.706	40.379	10.001
6	6.4745	0.9505	-3.0465	2.8075	1.3895	6.7945	-0.1693	0.3466	-0.2335	-0.0096	0.3289	0.0234	0.3382	0.8284	-0.1596	0.2901	0.2333	-0.0521	0.4625	-0.0218	0.4528	-62.052	19.097	7.843
7	2.2134	-0.5315	0.2292	3.9054	0.4731	5.3149	0.0716	-0.3129	-0.0122	0.2949	0.1202	-0.2656	0.247	1.279	-0.1919	0.1851	0.0561	0.002	0.3842	-0.0919	0.2851	-64.992	28.126	16.966
8	3.6609	-0.0465	1.853	4.381	-1.5148	2.7714	0.2717	-0.2899	-0.6918	0.1802	-0.1135	-0.1529	1.0939	0.858	-0.1581	0.8457	0.7304	-0.039	0.7239	0.0907	0.4407	-58.645	9.985	18.808
9	2.3123	0.6068	0.1445	1.8258	1.2792	5.486	-0.0594	-0.2035	0.3303	0.1182	0.1778	0.3443	-0.8279	-0.0693	-0.1184	0.4394	0.0526	0.019	0.0622	0.0337	0.3531	-80.644	42.532	16.725
10	2.5176	-1.4145	-1.8205	2.5052	0.1993	5.2748	-0.26	-0.2059	-0.1972	0.1894	0.1381	-0.2689	0.32	0.0889	0.1218	0.2535	-0.0272	0.038	0.2153	0.0368	0.1873	-91.812	25.768	37.474
11	3.9521	-1.8449	-0.1483	2.1826	0.1189	6.9481	-0.3731	-0.1538	-0.705	0.0947	0.1405	-0.1647	1.4394	0.7864	0.2327	0.5139	0.0993	0.1526	0.1553	0.0626	0.368	-83.352	11.88	32.964
12	1.986	0.9647	3.1388	4.2239	1.854	4.9975	-0.025	0.7711	-0.2937	0.8394	0.6597	-0.4567	0.3107	1.2703	-0.6348	0.6168	0.1859	0.1755	0.4332	-0.1437	0.3958	-82.234	5.81	15.271

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 92
2	X-RAY DIFFRACTION	2	A	93 - 107
3	X-RAY DIFFRACTION	3	A	108 - 269
4	X-RAY DIFFRACTION	4	A	270 - 342
5	X-RAY DIFFRACTION	5	B	1 - 101
6	X-RAY DIFFRACTION	6	B	102 - 139
7	X-RAY DIFFRACTION	7	B	140 - 239
8	X-RAY DIFFRACTION	8	B	240 - 322
9	X-RAY DIFFRACTION	9	C	1 - 103
10	X-RAY DIFFRACTION	10	C	104 - 197
11	X-RAY DIFFRACTION	11	C	198 - 335
12	X-RAY DIFFRACTION	12	C	336 - 342

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