PDB-6g80: Structure of Mycobacterium hassiacum MeT1 from orthorhombic crystals.

ID or keywords:

Entry

Database: PDB / ID: 6g80

Title

Structure of Mycobacterium hassiacum MeT1 from orthorhombic crystals.

Components

Methyltransferase domain protein

Keywords

TRANSFERASE / 3-O-methyltransferase

Function / homology

MMP 1-O-methyltransferase /

Methyltransferase domain /

methyltransferase activity /

methylation / carbohydrate metabolic process / S-adenosyl-L-methionine-dependent methyltransferase superfamily /

metal ion binding /

S-ADENOSYL-L-HOMOCYSTEINE / MMP 1-O-methyltransferase

Function and homology information

Biological species

Mycobacterium hassiacum

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.05 Å

Authors

Pereira, P.J.B. / Ripoll-Rozada, J.

Funding support

1items

Citation

Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2019
Title: Biosynthesis of mycobacterial methylmannose polysaccharides requires a unique 1-O-methyltransferase specific for 3-O-methylated mannosides.
Authors: Ripoll-Rozada, J. / Costa, M. / Manso, J.A. / Maranha, A. / Miranda, V. / Sequeira, A. / Ventura, M.R. / Macedo-Ribeiro, S. / Pereira, P.J.B. / Empadinhas, N.

History

Deposition	Apr 6, 2018	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jan 16, 2019	Provider: repository / Type: Initial release
Revision 1.1	Jan 23, 2019	Group: Data collection / Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2	May 8, 2024	Group: Advisory / Data collection / Database references Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	6g80.cif.gz	354.5 KB	Display	PDBx/mmCIF format
PDB format	pdb6g80.ent.gz	292.2 KB	Display	PDB format
PDBx/mmJSON format	6g80.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/g8/6g80 ftp://data.pdbj.org/pub/pdb/validation_reports/g8/6g80	HTTPS FTP

-
Related structure data

Related structure data	6g7dC 6h40C C: citing same article (ref.)
Similar structure data	4o47-d 1jvn-2 1r9z-d 2qvz-d 6xuq-d 3bwa-d 2o95-d 3hxz-2 1fm6-1 1k6w-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) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Methyltransferase domain protein

B: Methyltransferase domain protein

M: Methyltransferase domain protein

C: Methyltransferase domain protein

hetero molecules

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

1

A: Methyltransferase domain protein

B: Methyltransferase domain protein

hetero molecules

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

2

C: Methyltransferase domain protein

hetero molecules

M: Methyltransferase domain protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	117.150, 119.720, 145.000
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

#1: Protein	Methyltransferase domain protein Mass: 25445.342 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium hassiacum (strain DSM 44199 / CIP 105218 / JCM 12690 / 3849) (bacteria) Strain: DSM 44199 / CIP 105218 / JCM 12690 / 3849 / Gene: C731_4163 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: K5B7F3
#2: Chemical	ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₁₄H₂₀N₆O₅S
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 144 / 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: 2.5 Å³/Da / Density % sol: 50.75 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 0.04 M potassium phosphate monobasic, 16% (wt/vol) PEG 8000, 20% (vol/vol) glycerol.

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9724 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 22, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9724 Å / Relative weight: 1
Reflection	Resolution: 2.05→46.2 Å / Num. obs: 63196 / % possible obs: 98.7 % / Redundancy: 6.5 % / CC_1/2: 0.999 / R_rim(I) all: 0.061 / Net I/σ(I): 17.05
Reflection shell	Resolution: 2.05→2.07 Å / CC_1/2: 0.514 / R_rim(I) all: 1.513

-
Processing

Software

Name	Version	Classification
PHENIX	(1.13_2998: ???)	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.05→46.16 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.09 / Phase error: 25.85

	R_factor	Num. reflection	% reflection
R_free	0.2362	6081	5 %
R_work	0.1922	-	-
obs	0.1943	63182	98.39 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 2.05→46.16 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6727	0	84	144	6955

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	7035
X-RAY DIFFRACTION	f_angle_d	0.887	9588
X-RAY DIFFRACTION	f_dihedral_angle_d	17.229	4023
X-RAY DIFFRACTION	f_chiral_restr	0.06	1032
X-RAY DIFFRACTION	f_plane_restr	0.005	1264

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 (%)
2.05-2.0733	0.389	211	0.3909	3855	X-RAY DIFFRACTION	99
2.0733-2.0977	0.3949	208	0.3637	3864	X-RAY DIFFRACTION	99
2.0977-2.1233	0.3468	206	0.3275	3856	X-RAY DIFFRACTION	100
2.1233-2.1502	0.3361	231	0.3119	3959	X-RAY DIFFRACTION	100
2.1502-2.1785	0.3203	221	0.3	3828	X-RAY DIFFRACTION	100
2.1785-2.2083	0.2949	221	0.281	3935	X-RAY DIFFRACTION	100
2.2083-2.2399	0.3148	194	0.2724	3903	X-RAY DIFFRACTION	100
2.2399-2.2733	0.3552	141	0.3002	2227	X-RAY DIFFRACTION	58
2.2733-2.3088	0.3158	181	0.2701	3932	X-RAY DIFFRACTION	100
2.3088-2.3467	0.321	188	0.2624	3914	X-RAY DIFFRACTION	100
2.3467-2.3871	0.3061	213	0.2669	3954	X-RAY DIFFRACTION	100
2.3871-2.4305	0.2856	213	0.2431	3866	X-RAY DIFFRACTION	100
2.4305-2.4773	0.3517	238	0.251	3897	X-RAY DIFFRACTION	100
2.4773-2.5278	0.3195	200	0.2415	3901	X-RAY DIFFRACTION	100
2.5278-2.5828	0.3011	208	0.2226	3897	X-RAY DIFFRACTION	100
2.5828-2.6429	0.2541	257	0.2167	3864	X-RAY DIFFRACTION	100
2.6429-2.709	0.2516	224	0.2045	3937	X-RAY DIFFRACTION	100
2.709-2.7822	0.2416	189	0.2044	3913	X-RAY DIFFRACTION	100
2.7822-2.8641	0.2495	183	0.2054	3927	X-RAY DIFFRACTION	100
2.8641-2.9565	0.2441	186	0.2115	3927	X-RAY DIFFRACTION	100
2.9565-3.0621	0.2334	185	0.1881	3909	X-RAY DIFFRACTION	100
3.0621-3.1847	0.2587	225	0.1959	3911	X-RAY DIFFRACTION	100
3.1847-3.3296	0.2292	239	0.1927	3898	X-RAY DIFFRACTION	100
3.3296-3.5051	0.2239	201	0.1813	3910	X-RAY DIFFRACTION	100
3.5051-3.7246	0.2063	174	0.1647	3934	X-RAY DIFFRACTION	100
3.7246-4.012	0.2062	191	0.1579	3905	X-RAY DIFFRACTION	100
4.012-4.4155	0.1776	172	0.1522	3947	X-RAY DIFFRACTION	100
4.4155-5.0537	0.1755	178	0.1509	3928	X-RAY DIFFRACTION	100
5.0537-6.3645	0.2253	188	0.1824	3923	X-RAY DIFFRACTION	100
6.3645-46.1712	0.2273	215	0.1826	3901	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	8.221	-0.1469	-0.0603	6.8118	-1.4671	8.2566	-0.3901	-0.0253	0.2694	1.1323	0.4455	0.9877	-0.2247	-0.4087	-0.1073	0.6344	0.0705	0.2087	0.3212	0.0045	0.5937	24.3156	15.6891	-33.5439
2	2.0691	1.2022	1.6973	2.2633	3.5136	5.8047	-0.1932	0.0829	0.0178	-0.8873	0.4572	0.2613	-0.5713	0.1284	-0.2491	0.5548	-0.0083	0.0491	0.3509	0.0533	0.3812	27.2835	14.0427	-46.1577
3	3.4726	-0.4703	2.2692	4.4377	-0.4944	5.4379	0.048	0.0602	-0.0368	0.0016	-0.0383	0.2045	-0.0768	-0.1396	-0.0035	0.4718	-0.0035	0.0938	0.2656	0.0132	0.3624	28.7391	6.6086	-38.9369
4	2.0284	-1.31	-0.8069	2.7085	-1.6424	3.974	0.3315	-0.385	0.4331	0.9621	-0.2174	-0.3389	-0.1285	0.6464	-0.0984	0.6015	-0.0111	0.1152	0.4928	-0.0206	0.554	40.2553	11.5445	-29.4958
5	2.16	-0.9979	0.4807	3.7063	-1.7979	2.3682	-0.1201	-0.0628	0.2706	0.3391	0.0104	-0.1902	-0.3105	0.0593	0.1151	0.5147	-0.0059	0.0834	0.2667	-0.0334	0.3778	35.7244	4.0379	-31.5766
6	5.4946	4.1916	1.5973	9.1321	-0.5853	4.7461	-0.1196	0.3717	0.0605	-0.3996	-0.5963	-1.1106	0.6783	0.9333	0.4982	0.5413	0.1234	0.2699	0.5224	0.1688	0.8404	47.1478	4.641	-42.9792
7	1.8009	0.8877	0.0749	4.1943	-0.6793	1.9568	-0.1389	0.1784	-0.0823	-0.7278	-0.0916	-0.8256	0.1981	0.4203	0.2351	0.7099	0.0427	0.2364	0.4784	0.0724	0.5076	42.5814	12.2861	-50.5674
8	4.8678	-1.4281	-0.9796	6.001	1.3968	6.4126	-0.0185	-0.5392	-0.1925	0.6563	0.0346	-0.6115	0.1634	0.5357	-0.0245	0.4474	0.0206	-0.0055	0.3692	0.0629	0.5011	44.0987	-15.7711	-20.8105
9	7.7723	-3.169	1.5015	6.03	0.5319	6.3865	0.1116	-0.4365	-1.158	0.6945	-0.2327	0.8084	-0.4371	-0.9494	0.2766	0.5297	0.0255	0.1201	0.3799	0.0324	0.5521	28.5783	-9.1977	-25.3168
10	1.4878	-0.4555	0.5888	5.3074	0.9801	1.9535	-0.1017	-0.2141	-0.1608	0.4053	-0.0415	0.0796	0.0237	-0.0978	0.1527	0.5021	0.0008	0.0977	0.3581	0.0158	0.3644	32.3933	-6.8645	-24.0017
11	3.9655	1.3793	-2.5751	4.2299	-0.3312	4.321	-0.1058	0.1533	-0.147	-0.4363	0.0328	0.1676	0.2612	-0.0886	0.0747	0.443	0.043	0.0178	0.2655	-0.0159	0.3853	30.4832	-27.0887	-33.1774
12	1.7385	0.2437	0.8364	2.0132	-2.0071	7.0876	0.1183	-0.1929	0.3525	-0.03	-0.1255	-0.1113	0.2266	0.4786	0.0763	0.2732	0.0543	0.0025	0.4112	-0.0927	0.4708	18.1379	28.1624	1.1396
13	3.712	0.1735	-1.0014	1.9149	0.6875	2.1888	-0.1303	0.2936	0.0129	-0.1193	0.0466	-0.1488	0.2055	-0.0325	0.0892	0.3506	0.0244	-0.0105	0.428	-0.0522	0.3544	15.2739	20.7379	-9.4591
14	5.8526	-0.0543	-2.1266	3.6934	0.3593	5.6474	-0.0505	0.9141	0.9983	-0.2408	0.2533	0.1974	-0.5307	-0.1357	-0.212	0.3728	-0.044	-0.0822	0.5648	0.1176	0.596	51.3904	46.6204	-13.4443
15	7.298	0.7075	0.4566	1.2865	-2.5301	5.5213	-0.1296	1.0025	-0.8932	-0.4183	0.2288	0.9025	0.8165	-0.2573	-0.0049	0.396	-0.0685	-0.1077	0.6518	-0.1061	0.6757	55.4859	31.5295	-10.7294
16	5.3883	-0.5933	0.6145	1.9927	-0.5476	3.1758	0.0015	0.6967	-0.1972	-0.3852	-0.0218	0.12	0.0263	0.0009	0.0153	0.3075	-0.0456	-0.0045	0.4938	-0.0905	0.4351	58.2274	35.357	-10.7432
17	8.6641	2.0776	5.1	2.9346	1.5495	6.19	0.0005	-0.1742	-0.0756	-0.0703	0.0768	0.2526	-0.0156	-0.3566	-0.0499	0.2955	-0.0159	0.0665	0.5185	-0.0106	0.4581	40.151	35.0153	-3.9885

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 6 through 22 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 23 through 36 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 37 through 63 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 64 through 87 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 88 through 145 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 146 through 159 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 160 through 223 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 4 through 63 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 64 through 81 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 82 through 145 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 146 through 229 )
12	X-RAY DIFFRACTION	12	chain 'M' and (resid 6 through 100 )
13	X-RAY DIFFRACTION	13	chain 'M' and (resid 101 through 223 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 6 through 63 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 64 through 81 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 82 through 145 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 146 through 219 )

-
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