PDB-5y4r: Structure of a methyltransferase complex

ID or keywords:

Entry

Database: PDB / ID: 5y4r

Title

Structure of a methyltransferase complex

Components

Chemotaxis protein methyltransferase 1
Cyclic diguanosine monophosphate-binding protein PA4608

Keywords

TRANSFERASE/PROTEIN BINDING / Complex / TRANSFERASE-PROTEIN BINDING complex

Function / homology

Function and homology information

protein-glutamate O-methyltransferase / protein-glutamate O-methyltransferase activity / protein methyltransferase activity / cyclic-di-GMP binding / methylation
Similarity search - Function

Biological species

Pseudomonas aeruginosa str. PAO1 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.298 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 ...Data collection / Database references / Refinement description / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5y4r.cif.gz	341.8 KB	Display	PDBx/mmCIF format
PDB format	pdb5y4r.ent.gz	278.8 KB	Display	PDB format
PDBx/mmJSON format	5y4r.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	5y4r_validation.pdf.gz	1.9 MB	Display	wwPDB validaton report
Full document	5y4r_full_validation.pdf.gz	2 MB	Display
Data in XML	5y4r_validation.xml.gz	34.9 KB	Display
Data in CIF	5y4r_validation.cif.gz	46.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/y4/5y4r ftp://data.pdbj.org/pub/pdb/validation_reports/y4/5y4r	HTTPS FTP

-
Related structure data

Related structure data	5y4sC 5ftwS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4wnq-1 2w5f-2 5xly-d 6wt8-d 5xu6-4 4h38-d 2w5f-1 4uat-d 4rnz-d 2wys-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) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#254 - Feb 2021 Cellulose Synthase similarity (2) #130 - Oct 2010 Riboswitches similarity (1)

Deposited unit

A: Chemotaxis protein methyltransferase 1

D: Cyclic diguanosine monophosphate-binding protein PA4608

B: Chemotaxis protein methyltransferase 1

C: Cyclic diguanosine monophosphate-binding protein PA4608

hetero molecules

104 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Chemotaxis protein methyltransferase 1

D: Cyclic diguanosine monophosphate-binding protein PA4608

hetero molecules

defined by author&software
Evidence: assay for oligomerization
51.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Chemotaxis protein methyltransferase 1

C: Cyclic diguanosine monophosphate-binding protein PA4608

hetero molecules

defined by author&software
Evidence: assay for oligomerization
52 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	88.521, 98.927, 110.646
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Chemotaxis protein methyltransferase 1 Mass: 33023.848 Da / Num. of mol.: 2 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
#2: Protein	Cyclic diguanosine monophosphate-binding protein PA4608 / MapZ / c-di-GMP-binding protein PA4608 / Pilz domain-containing protein PA4608 Mass: 16932.779 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa str. PAO1 (bacteria) Strain: PAO1 / Gene: PA4608 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HVI1
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-C2E / 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) / c-di-GMP / Cyclic diguanosine monophosphate Mass: 690.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₀H₂₄N₁₀O₁₄P₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 179 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.42 Å³/Da / Density % sol: 49.27 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: Bis-Tris, PEG 3350, lithium salfate

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953726 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 25, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.953726 Å / Relative weight: 1
Reflection	Resolution: 2.298→50 Å / Num. obs: 43900 / % possible obs: 99.8 % / Redundancy: 6.75 % / CC_1/2: 0.998 / Net I/σ(I): 12.64
Reflection shell	Resolution: 2.3→2.44 Å / Redundancy: 6.91 % / Mean I/σ(I) obs: 1.43 / Num. unique obs: 6939 / CC_1/2: 0.568 / % possible all: 99

-
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: 5FTW

5ftw

Resolution: 2.298→48.285 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 26.04 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2396	4329	9.86 %
R_work	0.1927	-	-
obs	0.1973	43897	99.8 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.298→48.285 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6230	0	244	179	6653

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	6600
X-RAY DIFFRACTION	f_angle_d	0.964	8955
X-RAY DIFFRACTION	f_dihedral_angle_d	13.624	2405
X-RAY DIFFRACTION	f_chiral_restr	0.036	970
X-RAY DIFFRACTION	f_plane_restr	0.004	1121

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 (%)
2.2976-2.3237	0.3593	135	0.3342	1240	X-RAY DIFFRACTION	95
2.3237-2.351	0.3306	144	0.2889	1286	X-RAY DIFFRACTION	100
2.351-2.3797	0.3627	149	0.2637	1299	X-RAY DIFFRACTION	100
2.3797-2.4098	0.3429	150	0.2822	1300	X-RAY DIFFRACTION	100
2.4098-2.4415	0.3505	146	0.27	1287	X-RAY DIFFRACTION	100
2.4415-2.475	0.3032	140	0.2623	1338	X-RAY DIFFRACTION	100
2.475-2.5103	0.3339	158	0.2616	1280	X-RAY DIFFRACTION	100
2.5103-2.5478	0.2849	131	0.2523	1316	X-RAY DIFFRACTION	100
2.5478-2.5876	0.356	132	0.2551	1295	X-RAY DIFFRACTION	100
2.5876-2.63	0.3264	156	0.2586	1300	X-RAY DIFFRACTION	100
2.63-2.6754	0.2835	133	0.2586	1323	X-RAY DIFFRACTION	100
2.6754-2.724	0.3032	157	0.2488	1283	X-RAY DIFFRACTION	100
2.724-2.7764	0.3495	143	0.2566	1306	X-RAY DIFFRACTION	100
2.7764-2.8331	0.2941	149	0.2481	1341	X-RAY DIFFRACTION	100
2.8331-2.8947	0.3265	132	0.2631	1304	X-RAY DIFFRACTION	100
2.8947-2.962	0.3007	141	0.235	1307	X-RAY DIFFRACTION	100
2.962-3.0361	0.2784	146	0.233	1305	X-RAY DIFFRACTION	100
3.0361-3.1182	0.2948	137	0.2274	1317	X-RAY DIFFRACTION	100
3.1182-3.2099	0.2982	145	0.2197	1317	X-RAY DIFFRACTION	100
3.2099-3.3135	0.276	148	0.2197	1325	X-RAY DIFFRACTION	100
3.3135-3.4319	0.2625	137	0.2104	1312	X-RAY DIFFRACTION	100
3.4319-3.5692	0.2529	145	0.1887	1331	X-RAY DIFFRACTION	100
3.5692-3.7316	0.224	147	0.1844	1325	X-RAY DIFFRACTION	100
3.7316-3.9283	0.1879	140	0.162	1336	X-RAY DIFFRACTION	100
3.9283-4.1743	0.1956	149	0.152	1323	X-RAY DIFFRACTION	100
4.1743-4.4963	0.1847	150	0.1445	1339	X-RAY DIFFRACTION	100
4.4963-4.9484	0.201	132	0.1411	1378	X-RAY DIFFRACTION	100
4.9484-5.6635	0.2016	144	0.1626	1336	X-RAY DIFFRACTION	100
5.6635-7.1318	0.2019	145	0.1713	1378	X-RAY DIFFRACTION	100
7.1318-48.2961	0.1751	168	0.1528	1441	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	6.1191	-1.3009	-5.3261	5.6674	4.0119	6.7233	-0.2639	0.022	-0.9362	0.2221	-0.2088	0.8457	0.6868	-0.394	0.3793	0.5614	-0.0727	-0.1461	0.4943	0.0171	0.6502	-28.6586	4.5937	-21.8095
2	6.1149	1.4096	3.3049	2.1704	1.1148	5.0038	0.1897	-0.5725	0.2294	0.2194	-0.1892	0.0753	0.0399	-0.1183	0.0026	0.4058	0.0663	0.0517	0.4128	-0.0025	0.2948	-6.1581	22.9107	-9.3517
3	3.3404	0.6521	-0.8145	3.2761	-0.6952	3.1986	-0.0301	-0.2819	-0.1274	0.1527	-0.014	0.1569	0.1226	-0.1336	0.0655	0.3128	0.0724	-0.0369	0.2925	-0.0244	0.2821	-4.4669	23.3025	-14.3001
4	3.8639	0.635	-2.2564	3.6754	1.5571	2.3454	-0.2518	-0.0606	0.4626	-0.3437	0.0536	0.433	-0.6153	-0.4091	0.2793	0.7009	0.0089	-0.139	0.3032	0.0847	0.451	-15.3908	20.8945	-41.9842
5	6.1866	1.599	-4.7491	6.5494	3.1867	7.3984	0.2824	0.1359	-0.4332	-0.1647	-0.0699	-0.6801	0.7255	0.2963	-0.2837	0.7301	0.1298	-0.1952	0.4679	0.0054	0.3453	-5.3526	8.4199	-42.3913
6	5.3401	-0.1546	1.9686	5.5714	1.8318	1.8974	0.6031	0.5363	-0.7044	-0.0155	0.0983	-0.0828	1.522	0.3415	-0.6135	0.8844	0.1328	-0.1103	0.4681	-0.0807	0.459	-7.5137	6.1176	-43.0001
7	5.0867	1.2118	-2.8426	3.464	0.2991	4.7024	0.1534	0.3047	-0.1603	-0.375	-0.3231	0.1385	0.4217	-0.2793	0.1445	0.6009	0.0966	-0.158	0.3849	0.0102	0.3905	-13.6366	13.8034	-34.4852
8	5.3331	2.0472	5.3119	2.3688	2.0763	5.4166	-0.0237	-0.3093	0.716	0.0405	-0.8161	1.9617	0.6427	-0.7353	0.7005	0.5492	-0.014	0.0294	0.719	-0.031	0.6705	-25.486	18.2491	-33.8925
9	4.2021	3.3336	2.3387	4.9675	-0.418	3.397	0.0031	0.0833	0.2054	0.2328	0.0523	0.0048	-0.3435	0.6185	-0.0165	0.481	-0.0482	0.0572	0.5468	-0.1006	0.3464	37.3367	22.4954	-19.6665
10	3.8926	0.2796	-0.7081	4.1005	0.067	3.8563	-0.1135	-0.7044	-0.1767	0.5829	0.2074	-0.4417	0.2566	0.3393	-0.0629	0.5063	0.0808	-0.0774	0.4015	-0.007	0.3893	17.4507	-0.0687	-16.8739
11	5.6262	2.8052	0.0143	7.048	-3.0817	3.4258	0.276	1.1586	0.1539	-0.4099	0.007	-0.5423	0.5683	-0.048	-0.2047	0.5411	-0.0156	0.0769	0.396	-0.1135	0.4006	28.6898	15.7219	-43.8456
12	8.0288	-4.5745	2.3676	9.7208	-0.6477	7.6954	-0.0778	0.581	0.3275	-0.1222	0.0471	0.2348	-0.4118	-0.4536	0.0336	0.4017	-0.1067	0.0709	0.442	0.0344	0.3027	16.865	26.0519	-39.9356
13	3.6855	2.7411	5.7222	9.4837	3.9145	8.8636	-0.5809	0.9216	1.6008	-1.5003	0.3742	1.0053	-1.4036	0.2696	0.3601	0.9412	0.0393	0.1144	0.7702	0.1885	0.7086	16.3952	34.608	-46.1902
14	3.7359	1.347	-1.5521	4.6688	-1.2955	5.7989	0.1313	-0.0525	0.4496	0.2146	0.1955	-0.0444	-0.7116	0.3738	-0.1663	0.3578	-0.0234	0.0242	0.2804	0.0294	0.3041	19.8824	25.4383	-36.4326
15	2.3094	-0.4303	1.6865	5.7743	-2.2581	7.8989	-0.122	0.1138	0.1466	-0.0032	0.3113	-0.1239	-0.1991	-0.2705	-0.1661	0.2125	-0.0741	0.0587	0.3654	-0.0388	0.3522	25.7251	20.2988	-34.3748
16	5.4148	5.5672	-0.4201	5.7796	-0.7852	2.6796	0.2327	-0.0327	-1.0114	-0.3246	0.5355	-1.7233	0.3572	1.4892	-0.4387	0.5549	0.0302	0.0222	0.8384	-0.3269	0.7869	37.7451	14.7098	-34.6472

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 57 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 58 through 147 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 148 through 274 )
4	X-RAY DIFFRACTION	4	chain 'D' and (resid 6 through 18 )
5	X-RAY DIFFRACTION	5	chain 'D' and (resid 19 through 44 )
6	X-RAY DIFFRACTION	6	chain 'D' and (resid 45 through 79 )
7	X-RAY DIFFRACTION	7	chain 'D' and (resid 80 through 108 )
8	X-RAY DIFFRACTION	8	chain 'D' and (resid 109 through 124 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 3 through 80 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 81 through 274 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 6 through 18 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 19 through 44 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 45 through 56 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 57 through 79 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 80 through 106 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 107 through 123 )

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi