PDB-5y4s: Structure of a methyltransferase complex

ID or keywords:

Entry

Database: PDB / ID: 5y4s

Title

Structure of a methyltransferase complex

Components

Chemotaxis protein methyltransferase 1

Keywords

TRANSFERASE

Function / homology

Function and homology information

protein-glutamate O-methyltransferase / protein-glutamate O-methyltransferase activity / methylation
Similarity search - Function

Biological species

Pseudomonas aeruginosa str. PAO1 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.405 Å

Authors

Yan, X. / Xin, L. / Tan, Y.J. / Jin, S. / Liang, Z.X. / Gao, Y.G.

Funding support

Singapore, 1items

Citation

Journal: J. Biol. Chem. / Year: 2018
Title: Structural analyses unravel the molecular mechanism of cyclic di-GMP regulation of bacterial chemotaxis via a PilZ adaptor protein.
Authors: Yan, X.F. / Xin, L. / Yen, J.T. / Zeng, Y. / Jin, S. / Cheang, Q.W. / Fong, R.A.C.Y. / Chiam, K.H. / Liang, Z.X. / Gao, Y.G.

History

Deposition	Aug 4, 2017	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Nov 29, 2017	Provider: repository / Type: Initial release
Revision 1.1	Jan 17, 2018	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.2	Nov 22, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5y4s.cif.gz	1012.4 KB	Display	PDBx/mmCIF format
PDB format	pdb5y4s.ent.gz	853.6 KB	Display	PDB format
PDBx/mmJSON format	5y4s.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5y4s_validation.pdf.gz	534.8 KB	Display	wwPDB validaton report
Full document	5y4s_full_validation.pdf.gz	577.7 KB	Display
Data in XML	5y4s_validation.xml.gz	89.7 KB	Display
Data in CIF	5y4s_validation.cif.gz	118 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/y4/5y4s ftp://data.pdbj.org/pub/pdb/validation_reports/y4/5y4s	HTTPS FTP

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Related structure data

Related structure data	5y4rSC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3g6h-1 2fgj-1 2pjz-d 4fsa-d 4nap-3 3acw-d 4f6x-d 4nap-1 3ae0-1 5iug-d 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) 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) 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

5y4rSC

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Chemotaxis protein methyltransferase 1

B: Chemotaxis protein methyltransferase 1

C: Chemotaxis protein methyltransferase 1

D: Chemotaxis protein methyltransferase 1

E: Chemotaxis protein methyltransferase 1

F: Chemotaxis protein methyltransferase 1

G: Chemotaxis protein methyltransferase 1

H: Chemotaxis protein methyltransferase 1

I: Chemotaxis protein methyltransferase 1

J: Chemotaxis protein methyltransferase 1

330 kDa, 10 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Chemotaxis protein methyltransferase 1

defined by author
Evidence: assay for oligomerization
33 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Chemotaxis protein methyltransferase 1

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

3

C: Chemotaxis protein methyltransferase 1

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

4

D: Chemotaxis protein methyltransferase 1

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

5

E: Chemotaxis protein methyltransferase 1

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

6

F: Chemotaxis protein methyltransferase 1

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

7

G: Chemotaxis protein methyltransferase 1

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

8

H: Chemotaxis protein methyltransferase 1

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

9

I: Chemotaxis protein methyltransferase 1

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

10

J: Chemotaxis protein methyltransferase 1

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

Unit cell

Length a, b, c (Å)	279.545, 279.545, 138.799
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	80
Space group name H-M	I4₁

#1: Protein	Chemotaxis protein methyltransferase 1 Mass: 33023.848 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa str. PAO1 (bacteria) Strain: PAO1 / Gene: cheR1, PA3348 / Production host: Escherichia coli (E. coli) References: UniProt: O87131, protein-glutamate O-methyltransferase

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 4.11 Å³/Da / Density % sol: 70.04 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: sodium phosphate, potassium phosphate

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.97795 Å
Detector	Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Apr 30, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97795 Å / Relative weight: 1
Reflection	Resolution: 3.405→50 Å / Num. obs: 143861 / % possible obs: 99.9 % / Redundancy: 14.5 % / CC_1/2: 0.998 / Net I/σ(I): 13.82
Reflection shell	Resolution: 3.41→3.61 Å / Redundancy: 13.68 % / Mean I/σ(I) obs: 1.42 / Num. unique all: 23114 / CC_1/2: 0.531 / % possible all: 99.8

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5Y4R

5y4r

Resolution: 3.405→49.417 Å / Cross valid method: FREE R-VALUE / σ(F): 1.31 / Phase error: 33.81 / Stereochemistry target values: TWIN_LSQ_F
Details: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS

	R_factor	Num. reflection	% reflection
R_free	0.2928	13917	9.68 %
R_work	0.2598	-	-
obs	0.2626	143830	99.99 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 3.405→49.417 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	19440	0	0	0	19440

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	19807
X-RAY DIFFRACTION	f_angle_d	1.093	26908
X-RAY DIFFRACTION	f_dihedral_angle_d	12.512	6811
X-RAY DIFFRACTION	f_chiral_restr	0.043	3083
X-RAY DIFFRACTION	f_plane_restr	0.004	3523

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 (%)
3.4056-3.4643	0.3714	617	0.3407	6560	X-RAY DIFFRACTION	91
3.4643-3.5273	0.3552	760	0.3282	6400	X-RAY DIFFRACTION	89
3.5273-3.5951	0.3573	713	0.3236	6494	X-RAY DIFFRACTION	90
3.5951-3.6685	0.3444	625	0.3089	6628	X-RAY DIFFRACTION	91
3.6685-3.7482	0.3429	699	0.2947	6460	X-RAY DIFFRACTION	90
3.7482-3.8354	0.3227	650	0.296	6518	X-RAY DIFFRACTION	91
3.8354-3.9312	0.3371	733	0.2822	6461	X-RAY DIFFRACTION	90
3.9312-4.0375	0.3118	802	0.2857	6391	X-RAY DIFFRACTION	89
4.0375-4.1562	0.2901	688	0.2679	6455	X-RAY DIFFRACTION	90
4.1562-4.2903	0.2823	614	0.2611	6655	X-RAY DIFFRACTION	92
4.2903-4.4435	0.2983	751	0.2472	6410	X-RAY DIFFRACTION	90
4.4435-4.6212	0.273	693	0.2405	6452	X-RAY DIFFRACTION	90
4.6212-4.8314	0.2592	710	0.2457	6466	X-RAY DIFFRACTION	90
4.8314-5.0858	0.2729	703	0.2353	6518	X-RAY DIFFRACTION	90
5.0858-5.404	0.2895	682	0.2428	6490	X-RAY DIFFRACTION	90
5.404-5.8205	0.2969	646	0.2697	6568	X-RAY DIFFRACTION	91
5.8205-6.4049	0.3225	670	0.2835	6487	X-RAY DIFFRACTION	91
6.4049-7.3286	0.314	636	0.2889	6548	X-RAY DIFFRACTION	91
7.3286-9.2215	0.2681	796	0.2218	6399	X-RAY DIFFRACTION	89
9.2215-46.5952	0.2592	727	0.2287	6466	X-RAY DIFFRACTION	90

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	8.9855	-3.153	-2.0591	8.1136	2.9771	5.986	0.4058	0.3744	-1.0475	-0.2655	-0.8937	1.2668	0.263	-0.3437	0.3571	0.6567	0.0306	-0.1093	0.86	0.0229	1.1982	46.9096	345.1101	-55.3631
2	6.0766	1.6852	-0.1016	5.4627	-1.0453	7.0644	0.0976	1.5509	-1.088	-0.0166	0.1775	0.0579	-0.0527	0.2895	-0.4143	0.6942	0.1711	-0.0568	0.7544	-0.0386	0.6396	63.6942	337.0031	-37.381
3	5.6439	1.8291	-0.7748	5.5299	-2.3055	6.845	0.4267	0.179	-0.0712	0.1628	0.0866	-0.1208	-0.1743	0.2299	-0.4638	0.5571	0.1466	0.0257	0.542	-0.0214	0.5342	63.0109	343.4917	-32.048
4	6.4167	-3.0181	1.0294	8.9136	-2.6674	2.8419	-1.3976	-0.2019	-1.8711	0.8511	0.8523	0.478	-0.5775	-2.1995	-0.4008	1.4932	0.3522	-0.3064	1.6223	0.1907	1.5555	80.7054	284.2795	-9.1624
5	4.3852	-5.0306	2.8366	2.3631	-5.255	2.7725	-0.6494	-0.5856	-0.0713	1.0179	0.6548	-0.4841	0.227	-0.4381	0.2803	1.4015	0.3101	-0.544	1.2413	-0.0574	1.2043	86.1227	296.2869	-10.4899
6	4.1678	-1.9393	-0.2312	5.6875	-1.9369	5.426	-0.4041	-1.05	-0.1328	1.8184	0.5826	-0.3999	-0.3898	-0.0751	-0.135	1.7115	0.342	-0.6107	1.1227	0.0426	1.149	79.4376	313.9716	-9.036
7	7.8993	-0.7438	1.2381	6.116	-3.5949	8.713	0.6564	-0.9101	-0.4077	1.1951	-0.4744	-0.9112	0.0566	1.1014	0.1602	1.0029	-0.0707	-0.4189	0.9505	0.1458	1.0715	69.4114	314.826	-46.469
8	2.3726	-9.0673	1.9212	9.5677	-3.5799	5.1504	-0.3089	0.0322	-0.9092	0.5948	0.5785	0.4172	-0.1489	0.0802	-0.6587	0.9679	0.1104	-0.2382	0.913	0.051	1.268	55.2105	317.1858	-41.3799
9	2.2598	-2.6015	-0.904	6.1378	1.0557	5.2493	0.062	0.2045	-0.5361	-0.0485	0.1016	0.9292	0.3151	-0.8969	-0.1376	0.6082	-0.1179	-0.2093	0.8496	0.2368	1.4167	38.1031	317.728	-45.3593
10	7.1769	-2.7637	-4.6538	9.5506	-2.0626	4.6024	0.101	1.5598	0.1716	-1.5146	0.3096	0.1011	-0.0422	-0.9643	-0.26	0.9848	-0.0701	-0.2629	1.08	0.0481	1.0518	47.3544	314.9048	-59.8351
11	7.7675	-6.6443	0.2636	7.5101	0.0523	-0.2107	-0.1402	-0.5864	-1.4441	0.5066	0.3919	0.8135	0.7583	0.1221	-0.2277	1.3534	0.1577	-0.3315	1.0665	0.2197	1.4865	64.6771	297.865	-29.6183
12	7.3639	1.7702	1.4306	5.1796	-0.1458	3.6973	0.3297	0.6702	-0.7765	0.0386	0.2182	0.3339	0.8724	0.1557	-0.5488	1.4599	0.499	-0.4921	1.0353	0.0513	1.4663	76.4674	289.8957	-37.875
13	2.0431	-2.7121	0.745	1.9914	-3.8529	9.4147	1.1373	1.1993	-1.7688	1.3158	-1.6571	0.2426	1.4728	-0.3892	0.1874	1.16	-0.537	-0.2694	0.923	-0.0112	1.12	61.9949	313.7929	-63.7508
14	6.5819	3.3521	5.9986	2.7917	3.0406	5.6384	0.5168	0.0221	-1.2502	0.705	-0.0645	0.0013	1.0203	-0.4521	-0.4951	1.0166	-0.3708	-0.0759	1.1274	0.0856	1.2267	59.688	314.0879	-76.7317
15	6.3156	-0.6153	-1.5354	5.6209	1.0827	4.9948	0.6004	0.334	-0.4011	-0.0232	-0.3706	0.7279	0.3467	-1.2317	-0.1654	0.8439	-0.2433	-0.2711	1.0898	0.0154	0.8845	48.5112	317.22	-90.0731
16	1.0527	2.9999	1.0766	2.3988	2.6904	1.5795	-0.5524	0.7535	-0.6833	-0.0178	0.5765	-0.4585	0.1407	0.6662	-0.0621	1.4851	-0.5496	-0.1655	1.8708	-0.1851	2.1034	27.85	264.4775	-115.8187
17	4.3919	0.3022	-1.0346	4.2122	0.6993	4.2187	-0.2053	0.5952	-0.0188	-0.6692	-0.1302	0.2295	-0.8085	0.0317	0.3883	1.7652	-0.4791	-0.6224	1.5277	-0.3111	1.7064	29.6267	289.3697	-114.0931
18	8.223	-0.1212	-0.5046	8.3878	-1.9505	6.9288	0.3347	-0.6169	1.8876	0.8592	-0.3457	-0.3378	0.8906	0.7432	0.437	1.5179	0.2129	-0.2771	1.3004	0.1158	1.8622	132.1014	272.3602	-5.321
19	3.477	2.1097	-1.6319	2.469	0.0122	2.4185	0.0023	0.3359	-0.7675	-0.3338	-0.0437	-0.1311	0.094	0.0202	0.0304	1.4992	0.6065	-0.4731	1.3648	-0.0483	2.0061	111.9887	273.7137	-27.5622
20	3.0657	3.1139	-2.1066	3.309	-1.6183	5.1305	-0.6791	-0.3383	0.0648	0.1453	0.5827	-0.6477	-0.8849	0.7344	0.1448	1.8089	0.4606	-0.4992	1.4557	-0.0011	2.2328	126.3192	283.9238	-24.7142
21	4.5133	-0.8697	3.4695	5.8301	-1.6486	6.8833	-1.2297	0.0435	0.8667	0.7291	-0.2076	-1.377	-0.8541	0.7535	0.2476	1.1968	0.3162	-0.3998	1.4156	0.0049	1.729	103.5919	298.6352	-11.9894
22	2.9884	-0.7769	-2.2416	8.474	-0.9798	2.0644	-0.9664	-0.3853	-0.7728	0.0006	0.6474	0.1312	-0.6849	0.6706	-0.0328	1.1352	0.4143	-0.4168	1.3873	0.1599	1.9446	111.231	279.423	3.5925
23	2.8936	-0.7221	-0.4012	5.158	1.2964	3.6869	-0.259	-1.0592	-1.5465	0.3815	0.5456	0.6632	0.3629	0.3633	-0.006	1.4763	0.528	-0.2471	1.5099	0.5587	2.1512	102.5517	272.685	8.3182
24	5.3392	-0.2283	0.9545	2.2572	1.0838	4.3486	0.1803	-0.2598	-0.1476	-0.1824	0.1066	0.328	-1.0102	0.5215	-0.1572	1.598	0.4028	-0.5982	1.6536	0.2215	1.6492	108.1589	292.3084	9.5994
25	6.1333	4.6252	0.6308	7.3043	0.0355	1.4722	-0.1253	0.9051	-1.461	-0.412	0.4741	-1.5118	0.2345	-0.1734	-0.3491	1.9776	-0.3173	-0.6839	1.375	-0.3205	2.4882	49.2386	273.379	-99.4445
26	3.6175	0.0583	0.1037	2.7022	0.1589	2.4863	0.4077	-0.65	-1.5105	0.8473	-0.5357	-0.9789	0.3031	0.1099	0.0996	2.0988	-0.766	-0.8214	1.7736	0.109	2.7523	37.7964	261.7563	-88.4663
27	8.1031	5.4041	0.7236	3.369	0.7195	-0.0138	1.3559	-1.9294	-0.0424	1.352	-0.9831	-0.0275	0.7973	-0.3635	-0.2821	2.2841	-0.707	-0.5604	1.6615	-0.13	2.0406	48.7821	287.9672	-80.5406
28	4.2244	0.3901	-0.2357	6.3184	0.43	3.8491	0.8193	-0.6858	-1.5302	0.3593	0.0835	-0.7364	0.9316	0.2769	-0.8153	1.6068	-0.5341	-0.5349	1.3152	-0.1367	2.0712	76.9236	295.4422	-84.2833
29	2.9645	1.6922	-0.0263	6.1989	-0.9757	1.5059	1.2678	-1.8098	-1.8978	1.2296	-0.717	-0.2601	1.1483	-0.4783	-0.4601	2.6419	-0.9501	-1.0682	1.8706	0.5178	2.7224	70.4976	282.6201	-74.9812

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 5 through 66 )	A	5 - 66
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 67 through 98 )	A	67 - 98
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 99 through 274 )	A	99 - 274
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 5 through 52 )	B	5 - 52
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 53 through 80 )	B	53 - 80
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 81 through 273 )	B	81 - 273
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 5 through 60 )	C	5 - 60
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 61 through 80 )	C	61 - 80
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 81 through 238 )	C	81 - 238
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 239 through 274 )	C	239 - 274
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 6 through 113 )	D	6 - 113
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 114 through 273 )	D	114 - 273
13	X-RAY DIFFRACTION	13	chain 'E' and (resid 5 through 17 )	E	5 - 17
14	X-RAY DIFFRACTION	14	chain 'E' and (resid 18 through 98 )	E	18 - 98
15	X-RAY DIFFRACTION	15	chain 'E' and (resid 99 through 274 )	E	99 - 274
16	X-RAY DIFFRACTION	16	chain 'F' and (resid 5 through 80 )	F	5 - 80
17	X-RAY DIFFRACTION	17	chain 'F' and (resid 81 through 274 )	F	81 - 274
18	X-RAY DIFFRACTION	18	chain 'G' and (resid 5 through 66 )	G	5 - 66
19	X-RAY DIFFRACTION	19	chain 'G' and (resid 67 through 246 )	G	67 - 246
20	X-RAY DIFFRACTION	20	chain 'G' and (resid 247 through 274 )	G	247 - 274
21	X-RAY DIFFRACTION	21	chain 'H' and (resid 5 through 66 )	H	5 - 66
22	X-RAY DIFFRACTION	22	chain 'H' and (resid 67 through 98 )	H	67 - 98
23	X-RAY DIFFRACTION	23	chain 'H' and (resid 99 through 216 )	H	99 - 216
24	X-RAY DIFFRACTION	24	chain 'H' and (resid 217 through 274 )	H	217 - 274
25	X-RAY DIFFRACTION	25	chain 'I' and (resid 5 through 98 )	I	5 - 98
26	X-RAY DIFFRACTION	26	chain 'I' and (resid 99 through 274 )	I	99 - 274
27	X-RAY DIFFRACTION	27	chain 'J' and (resid 5 through 80 )	J	5 - 80
28	X-RAY DIFFRACTION	28	chain 'J' and (resid 81 through 187 )	J	81 - 187
29	X-RAY DIFFRACTION	29	chain 'J' and (resid 188 through 274 )	J	188 - 274

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