PDB-5eox: Pseudomonas aeruginosa PilM bound to ADP

ID or keywords:

Entry

Database: PDB / ID: 5eox

Title

Pseudomonas aeruginosa PilM bound to ADP

Components

Type 4 fimbrial biogenesis protein PilM

Keywords

PEPTIDE BINDING PROTEIN / PilM / actin-like / Type IV Pilus / T4P

Function / homology

Function and homology information

type IV pilus / type IV pilus assembly / type IV pilus-dependent motility / cell division / ATP binding / metal ion binding / cytoplasm
Similarity search - Function

Biological species

Pseudomonas aeruginosa (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.4 Å

Authors

McCallum, M. / Tammam, S. / Robinson, H. / Shah, M. / Calmettes, C. / Moraes, T. / Burrows, L.L. / Howell, P.L.

Citation

Journal: J.Biol.Chem. / Year: 2016
Title: PilN Binding Modulates the Structure and Binding Partners of the Pseudomonas aeruginosa Type IVa Pilus Protein PilM.
Authors: McCallum, M. / Tammam, S. / Little, D.J. / Robinson, H. / Koo, J. / Shah, M. / Calmettes, C. / Moraes, T.F. / Burrows, L.L. / Howell, P.L.

History

Deposition	Nov 10, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 27, 2016	Provider: repository / Type: Initial release
Revision 1.1	Jun 8, 2016	Group: Database references
Revision 1.2	Sep 27, 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5eox.cif.gz	275 KB	Display	PDBx/mmCIF format
PDB format	pdb5eox.ent.gz	222.8 KB	Display	PDB format
PDBx/mmJSON format	5eox.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5eox_validation.pdf.gz	1 MB	Display	wwPDB validaton report
Full document	5eox_full_validation.pdf.gz	1 MB	Display
Data in XML	5eox_validation.xml.gz	28 KB	Display
Data in CIF	5eox_validation.cif.gz	38 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/eo/5eox ftp://data.pdbj.org/pub/pdb/validation_reports/eo/5eox	HTTPS FTP

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Related structure data

Related structure data	5eouC 5eoySC 5eq6C C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5eoy-d 5wer-3 5i96-d 3zx2-1 6vg0-1 2nwa-3 2zdy-d 3zx3-1 1pjs-d 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 (5)

Deposited unit

A: Type 4 fimbrial biogenesis protein PilM

B: Type 4 fimbrial biogenesis protein PilM

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	41.562, 111.355, 150.384
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P22₁2₁

#1: Protein	Type 4 fimbrial biogenesis protein PilM Mass: 38301.578 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228) (bacteria) Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: pilM, PA5044 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: G3XD28
#2: Chemical	ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₅O₁₀P₂ / Comment: ADP, energy-carrying molecule*YM
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.27 Å³/Da / Density % sol: 45.85 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: PEG3350, magnesium chloride, Bis-Tris / PH range: 7

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 5, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.075 Å / Relative weight: 1
Reflection	Resolution: 2.4→46 Å / Num. obs: 34804 / % possible obs: 100 % / Redundancy: 11.7 % / R_sym value: 0.069 / Net I/σ(I): 30.6

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5EOY

5eoy

Resolution: 2.4→45.71 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.22 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2574	1376	4.91 %
R_work	0.2236	-	-
obs	0.2252	30127	99.84 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.4→45.71 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4978	0	56	88	5122

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	5087
X-RAY DIFFRACTION	f_angle_d	0.858	6937
X-RAY DIFFRACTION	f_dihedral_angle_d	13.474	1768
X-RAY DIFFRACTION	f_chiral_restr	0.03	872
X-RAY DIFFRACTION	f_plane_restr	0.004	888

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 (%)
2.4-2.4462	0.3479	164	0.3557	2798	X-RAY DIFFRACTION	99
2.4462-2.4961	0.3656	166	0.3307	2721	X-RAY DIFFRACTION	100
2.4961-2.5504	10000000	0	0.3164	2926	X-RAY DIFFRACTION	100
2.5504-2.6097	0.2986	163	0.3099	2783	X-RAY DIFFRACTION	99
2.6097-2.675	0.359	170	0.3071	2720	X-RAY DIFFRACTION	100
2.675-2.7473	0.3494	167	0.3041	2782	X-RAY DIFFRACTION	100
2.7473-2.8281	0.3956	160	0.2997	2753	X-RAY DIFFRACTION	100
2.8281-2.9194	0.3196	164	0.3051	2749	X-RAY DIFFRACTION	100
2.9194-3.0237	0.3434	164	0.2775	2755	X-RAY DIFFRACTION	100
3.0237-3.1447	0.3476	162	0.2655	2787	X-RAY DIFFRACTION	100
3.1447-3.2878	0.2623	164	0.2572	2741	X-RAY DIFFRACTION	100
3.2878-3.4611	10000000	0	0.2499	2964	X-RAY DIFFRACTION	100
3.4611-3.6779	0.2862	161	0.2197	2730	X-RAY DIFFRACTION	100
3.6779-3.9617	0.2477	160	0.1952	2770	X-RAY DIFFRACTION	100
3.9617-4.3601	0.2146	155	0.1821	2779	X-RAY DIFFRACTION	100
4.3601-4.9903	0.1915	155	0.1791	2772	X-RAY DIFFRACTION	100
4.9903-6.2847	0.2634	159	0.203	2771	X-RAY DIFFRACTION	100
6.2847-45.7183	0.2018	151	0.1888	2781	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	9.0135	0.702	-0.1201	8.3037	-2.8638	6.8087	-0.258	0.1581	-0.2166	-0.3825	0.0817	-0.003	0.3523	-0.5544	0.1579	0.3833	-0.0348	-0.0123	0.4315	-0.1352	0.3929	-43.4027	137.8846	2.8478
2	6.6134	2.2442	3.0571	1.1312	1.279	6.6517	-0.5156	0.4556	0.768	0.1377	0.0009	0.3812	-0.7105	0.2986	0.663	0.7189	-0.025	-0.0658	0.4925	0.0038	0.6367	-18.003	155.7964	6.1012
3	7.5829	1.2669	-0.354	8.0513	-1.9039	3.0314	-0.0043	0.4133	-0.4629	-0.2384	-0.0064	-0.6034	0.2213	0.0462	-0.0244	0.482	-0.0152	-0.0869	0.3861	-0.1189	0.394	-34.8269	143.2418	3.6047
4	8.1321	3.7444	0.8232	8.6381	3.2574	7.7711	0.1569	-0.1468	-0.2811	-0.3948	0.3687	-3.1993	-1.0214	0.4442	-0.6608	0.7458	-0.0036	0.3097	0.6048	-0.2829	1.6861	-23.9223	128.4008	-0.9742
5	8.4735	3.4365	4.7574	3.877	-0.8017	5.5134	0.086	1.2817	-0.9264	-1.6413	-0.1781	-0.3867	-1.0517	-0.9244	0.0897	1.4579	0.2238	0.2584	1.1895	-0.2966	0.8011	-42.6447	120.8616	-18.0972
6	3.001	0.3198	-1.1095	0.2069	-0.912	3.9417	-0.0389	0.859	-1.5037	-1.0888	0.3353	-2.7683	0.3044	0.8281	-0.0977	0.8048	-0.0433	0.4425	0.7682	-0.3116	1.8515	-24.0255	120.3084	-6.542
7	6.9407	-0.8523	-5.0694	9.1367	-1.1227	4.6201	-0.3359	-0.2335	-1.0005	0.7411	0.0957	-0.3831	0.6217	-0.1472	0.2349	0.5813	-0.017	-0.0751	0.4398	0.0191	0.4859	-38.818	128.5367	8.4175
8	2.5919	0.9303	1.1985	3.531	3.2676	3.1976	0.2602	0.0393	-0.2455	-2.1358	-0.1684	-1.329	-0.8299	-0.5195	-0.0855	0.7497	-0.0785	-0.0036	0.6946	0.2188	0.7157	-34.9871	148.4323	29.3436
9	2.5469	-0.8717	1.0908	5.0319	-4.1646	3.5019	-0.1738	-1.3432	0.6544	2.7276	-0.5871	-0.1089	-0.8867	-0.3216	0.7041	0.8424	0.1352	-0.0585	0.8641	-0.166	0.5458	-27.715	148.1976	8.1561
10	3.3755	-0.5475	2.6791	6.74	2.9924	8.7623	-0.2877	0.4292	0.2791	0.2753	-0.194	-0.2237	0.1125	0.8991	0.4637	0.443	-0.0104	-0.0684	0.5305	0.2123	0.6731	-18.7404	139.5461	36.8239
11	5.6893	-4.4317	5.6174	7.2128	-4.446	7.739	-0.6447	-0.5695	0.3137	0.6437	0.2989	-0.3515	-1.1418	-0.4998	0.4167	0.5879	0.0468	-0.002	0.4499	-0.0594	0.4701	-44.1114	157.2309	32.4731
12	7.4075	-0.1707	1.6601	7.5464	0.4601	1.6263	-0.0915	-0.1254	0.7078	0.576	-0.2955	0.2131	0.0093	0.1371	0.3599	0.6515	0.0535	-0.1079	0.4715	0.1507	0.5654	-27.6132	144.2789	35.4934
13	7.7197	-3.0476	-1.4269	8.7904	-5.7404	7.9494	-0.1207	0.7347	0.4186	0.4141	0.882	2.1811	-1.2722	-0.4995	-0.5693	0.592	-0.0086	0.2369	0.4358	0.1961	1.0964	-38.4701	130.0872	40.4047
14	6.3975	-0.0876	4.7117	6.4534	-2.4924	4.8327	0.0108	0.5277	-0.071	0.7868	-0.3238	-0.3611	-0.7118	0.8664	0.2575	0.9551	-0.3052	0.137	0.7633	-0.036	0.4294	-19.6635	123.6605	57.9259
15	7.0821	0.2623	-1.8083	2.8564	-0.9846	7.8542	0.3694	0.1613	0.3493	0.2997	0.3721	1.3212	-0.1223	-0.5777	-0.6446	0.5651	0.01	0.1544	0.3665	0.1167	0.9448	-38.9618	122.5955	46.1816
16	9.0559	1.3817	-3.7882	3.9351	3.5744	8.2529	0.0297	0.3817	0.0353	-0.7558	-0.2394	-0.0015	0.5741	0.7651	0.1416	0.439	0.0948	-0.0233	0.5037	0.103	0.384	-23.2708	129.9773	31.528

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 11 through 81)
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 82 through 147 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 148 through 182 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 183 through 223 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 224 through 265 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 266 through 318 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 319 through 354 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid -1 through 10)
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 0 through 7)
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 11 through 81)
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 82 through 147 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 148 through 182 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 183 through 223 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 224 through 265 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 266 through 318 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 319 through 354 )

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