PDB-7l9u: Crystal Structure of S-adenosylmethionine-dependent methyltransfe...

ID or keywords:

Entry

Database: PDB / ID: 7l9u

Title

Crystal Structure of S-adenosylmethionine-dependent methyltransferase UmaA from Mycobacterium tuberculosis in complex with a 12-mer PEG

Components

S-adenosylmethionine-dependent methyltransferase UmaA

Keywords

TRANSFERASE / SSGCID / S-adenosylmethionine-dependent methyltransferase / SAM-dependent methyltransferase / UmaA / Mycobacterium tuberculosis / short-chain fatty acid modification / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease

Function / homology

Function and homology information

lipid biosynthetic process / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / methylation / plasma membrane / cytoplasm
Similarity search - Function

Biological species

Mycobacterium tuberculosis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.55 Å

Authors

Seattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: to be published
Title: Crystal Structure of S-adenosylmethionine-dependent methyltransferase UmaA from Mycobacterium tuberculosis in complex with a 12-mer PEG
Authors: Abendroth, J. / Weiss, M.J. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.

History

Deposition	Jan 5, 2021	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 10, 2021	Provider: repository / Type: Initial release
Revision 1.1	Mar 6, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7l9u.cif.gz	166 KB	Display	PDBx/mmCIF format
PDB format	pdb7l9u.ent.gz	107.7 KB	Display	PDB format
PDBx/mmJSON format	7l9u.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7l9u_validation.pdf.gz	627.1 KB	Display	wwPDB validaton report
Full document	7l9u_full_validation.pdf.gz	627.8 KB	Display
Data in XML	7l9u_validation.xml.gz	15.7 KB	Display
Data in CIF	7l9u_validation.cif.gz	23.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/l9/7l9u ftp://data.pdbj.org/pub/pdb/validation_reports/l9/7l9u	HTTPS FTP

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Related structure data

Similar structure data	7lxi-d 5i2r-2 5i2r-3 5c1w-2 3d1r-d 4fcb-2 5ede-2 5c3r-3 5edg-2 5b4k-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: MytuD.00149.b

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: S-adenosylmethionine-dependent methyltransferase UmaA

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	103.020, 103.020, 49.760
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	154
Space group name H-M	P3₂21
Space group name Hall	P3₂2"
Symmetry operation	#1: x,y,z #2: -y,x-y,z+2/3 #3: -x+y,-x,z+1/3 #4: x-y,-y,-z+1/3 #5: -x,-x+y,-z+2/3 #6: y,x,-z

Components on special symmetry positions

ID	Model	Components
1	1	A-553- HOH

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Protein , 1 types, 1 molecules A

#1: Protein	S-adenosylmethionine-dependent methyltransferase UmaA / SAM-dependent methyltransferase UmaA Mass: 34162.746 Da / Num. of mol.: 1 / Fragment: MytuD.00149.b.B1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv / Gene: umaA, Rv0469, LH57_02505 / Plasmid: MytuD.00149.b.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q6MX39, Transferases; Transferring one-carbon groups; Methyltransferases

#1: Protein

S-adenosylmethionine-dependent methyltransferase UmaA / SAM-dependent methyltransferase UmaA

Mass: 34162.746 Da / Num. of mol.: 1 / Fragment: MytuD.00149.b.B1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv / Gene: umaA, Rv0469, LH57_02505 / Plasmid: MytuD.00149.b.B1 / Production host:

Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q6MX39, Transferases; Transferring one-carbon groups; Methyltransferases

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Non-polymers , 5 types, 316 molecules

#2: Chemical	ChemComp-12P / DODECAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 Mass: 546.646 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₄H₅₀O₁₃ / Comment: precipitant*YM
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-NO3 / NITRATE ION Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO₃
#5: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 311 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.23 Å³/Da / Density % sol: 45 %
Crystal grow	Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Microlytics MCSG1 screen, condition C9: 32% (w/V) PEG 4000, 800mM lithium chloride, 100mM Tris Base/ HCl pH 8.50: MytuD.00149.b.B1.PW38903, tray 318922c9, cryo: 15% EG, puck ynm8-4. For ...Details: Microlytics MCSG1 screen, condition C9: 32% (w/V) PEG 4000, 800mM lithium chloride, 100mM Tris Base/ HCl pH 8.50: MytuD.00149.b.B1.PW38903, tray 318922c9, cryo: 15% EG, puck ynm8-4. For phasing, a crystal from the same screen and well set up with 5mM AMPPNP/MgCl2 was incubated for 20sec in a solution of 10% saturated NaI in EG + 90% reservoir, followed by a 20sec soak in 20% of saturated NaI in EG + 80% reservoir: tray 318925c9, cryo: 20% EG + NaI: puck zxc1-11. Anomalous data were collected at the home source at CuKalpha radiation.

Crystal

Density Matthews: 2.23 Å³/Da / Density % sol: 45 %

Crystal grow

Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Microlytics MCSG1 screen, condition C9: 32% (w/V) PEG 4000, 800mM lithium chloride, 100mM Tris Base/ HCl pH 8.50: MytuD.00149.b.B1.PW38903, tray 318922c9, cryo: 15% EG, puck ynm8-4. For ...

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID	Serial crystal experiment
1	100	1	N
2		1

Diffraction source

Source	Site	Beamline	Type	ID	Wavelength (Å)
SYNCHROTRON	APS	21-ID-F		1	0.97872
ROTATING ANODE			RIGAKU FR-E+ SUPERBRIGHT	2	1.5418

Detector

Type	ID	Detector	Date	Details
RAYONIX MX-300	1	CCD	Dec 10, 2020	Beryllium Lenses
RIGAKU SATURN 944+	2	CCD	Dec 10, 2020

Radiation

ID	Monochromator	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	Diamond [111]	SINGLE WAVELENGTH	M	x-ray	1
2		SINGLE WAVELENGTH	M	x-ray	2

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97872	1
2	1.5418	1

Reflection

Resolution: 1.55→50 Å / Num. obs: 44265 / % possible obs: 99.8 % / Redundancy: 7.337 % / B_iso Wilson estimate: 31.363 Å² / CC_1/2: 1 / R_merge(I) obs: 0.034 / R_rim(I) all: 0.037 / Χ²: 0.948 / Net I/σ(I): 27.33

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
1.55-1.59	7.097	0.606	2.98	3260	0.853	0.653	100
1.59-1.63	7.359	0.454	4.1	3172	0.921	0.488	100
1.63-1.68	7.375	0.341	5.47	3094	0.955	0.366	100
1.68-1.73	7.38	0.257	7.26	2981	0.971	0.276	100
1.73-1.79	7.376	0.199	9.4	2899	0.984	0.214	100
1.79-1.85	7.411	0.145	12.85	2825	0.991	0.156	100
1.85-1.92	7.43	0.11	16.49	2699	0.995	0.118	100
1.92-2	7.404	0.082	21.74	2623	0.997	0.089	100
2-2.09	7.402	0.065	27.49	2491	0.998	0.07	100
2.09-2.19	7.419	0.053	32.83	2413	0.998	0.057	100
2.19-2.31	7.413	0.044	38.58	2281	0.999	0.047	99.9
2.31-2.45	7.393	0.04	43.26	2178	0.999	0.042	99.9
2.45-2.62	7.317	0.036	47.32	2049	0.999	0.038	99.9
2.62-2.83	7.372	0.032	52.53	1883	0.999	0.035	99.7
2.83-3.1	7.29	0.029	56.28	1780	0.999	0.031	99.8
3.1-3.47	7.321	0.025	61.36	1581	0.999	0.027	99.6
3.47-4	7.218	0.023	64.37	1399	0.999	0.025	99.1
4-4.9	7.22	0.022	64.9	1202	0.999	0.024	99
4.9-6.93	7.213	0.022	64.2	930	1	0.024	97.9
6.93-50	6.476	0.027	62.03	525	0.998	0.03	93.8

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Processing

Software

Name	Version	Classification
XDS		data reduction
XSCALE		data scaling
PHENIX	1.19rc4 4035	refinement
PDB_EXTRACT	3.27	data extraction
PHASER		phasing
PARROT		phasing
ARP/wARP		model building
Coot		model building

Refinement

Method to determine structure:

SAD / Resolution: 1.55→43.46 Å / SU ML: 0.155 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.4137
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1753	2055	4.64 %	0
R_work	0.1571	42198	-	-
obs	0.158	44253	99.81 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 30.89 Å²

Refinement step

Cycle: LAST / Resolution: 1.55→43.46 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2250	0	50	311	2611

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0089	2405
X-RAY DIFFRACTION	f_angle_d	0.978	3243
X-RAY DIFFRACTION	f_chiral_restr	0.0554	347
X-RAY DIFFRACTION	f_plane_restr	0.0081	419
X-RAY DIFFRACTION	f_dihedral_angle_d	15.7391	898

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 (%)
1.55-1.59	0.2823	116	0.241	2826	X-RAY DIFFRACTION	100
1.59-1.63	0.2383	110	0.2047	2805	X-RAY DIFFRACTION	100
1.63-1.67	0.1965	125	0.183	2789	X-RAY DIFFRACTION	99.97
1.67-1.72	0.2067	145	0.1683	2803	X-RAY DIFFRACTION	100
1.72-1.77	0.1946	109	0.1719	2833	X-RAY DIFFRACTION	100
1.77-1.84	0.186	116	0.1683	2810	X-RAY DIFFRACTION	100
1.84-1.91	0.2149	123	0.1843	2836	X-RAY DIFFRACTION	99.97
1.91-2	0.2396	164	0.1687	2736	X-RAY DIFFRACTION	99.97
2-2.1	0.1891	134	0.1622	2805	X-RAY DIFFRACTION	100
2.1-2.24	0.1967	168	0.1585	2807	X-RAY DIFFRACTION	100
2.24-2.41	0.1819	143	0.1567	2790	X-RAY DIFFRACTION	99.93
2.41-2.65	0.1901	150	0.169	2818	X-RAY DIFFRACTION	100
2.65-3.03	0.1846	152	0.1638	2815	X-RAY DIFFRACTION	99.76
3.03-3.82	0.1629	138	0.1421	2848	X-RAY DIFFRACTION	99.53
3.82-43.46	0.1374	162	0.1408	2877	X-RAY DIFFRACTION	98.13

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	1.96803082111	0.237436555329	0.891480399324	0.102091243747	0.135816485776	0.861750517578	0.171271824472	0.269190001011	0.192569466239	-0.405073693507	0.0409660465067	-0.89877428805	-0.379458470961	0.66290814769	-0.115789117773	0.333475518618	-0.121189645298	0.141553325307	0.390235389567	-0.0644271648131	0.63910938568	49.5461083149	14.3135471729	9.14337446055
2	1.17780394923	-0.706024845669	0.390407803479	1.77423393262	-0.235004870214	2.85492025087	-0.0212655341043	0.00378937475259	-0.00455241419254	0.021194988284	0.0107936350545	-0.00626378903272	0.0280162576651	-0.199609740413	0.0382578229868	0.14598111214	-0.0263013716722	0.0127468524561	0.158563640861	-0.00827227346783	0.160919869325	22.9667526373	11.4470233825	3.16376145914
3	1.25116250451	-0.425520699183	0.190764691398	2.23007986862	-0.159336743362	2.65325886008	0.0834378037991	0.235442780209	0.165555262959	-0.263197276357	-0.118627999321	-0.359530210916	-0.02217305814	0.189506117343	0.0376572288377	0.178549275974	-0.00636602494611	0.0667597230046	0.243235105374	0.0278527872185	0.209694396574	31.6183734884	12.0281272615	-8.26403597391
4	1.63020016675	0.075702073764	1.3203750745	1.74498919489	0.714676114843	3.40114619645	-0.136450712102	-0.0286874871542	0.404176843844	-0.0178375471532	0.0598128239645	-0.163982301841	-0.577932864	0.00578521319669	0.0572179442965	0.259347463365	-0.0267894876175	0.0290715840098	0.175742633221	0.022797265369	0.325269927657	30.7782767207	30.6638442961	6.5571830142
5	0.710627445255	-0.341306838146	1.82570244342	1.46286746981	-0.477857957394	4.12463279015	-0.243932619134	0.419098539066	0.596952403012	-0.281474812537	-0.165335246226	-0.771425458359	-0.390878915367	0.179858846543	0.09737303833	0.279744253885	-0.0260292690452	0.00455493114914	0.252101010868	0.0931448534366	0.4834130781	29.1777958133	32.2263655911	-3.17151590108
6	1.86706220566	-0.831604755241	0.912950734539	2.33960897295	-1.05501139544	1.47886291656	-0.0990176553005	-0.0455573415181	0.195885224789	0.227988741921	-0.00098360346372	-0.256771404675	-0.168670576719	0.0363073984754	0.123473811043	0.184961184496	-0.0194940221357	0.00561590068751	0.139366215096	-0.0286679286956	0.201353187677	31.2405430275	19.6482053176	11.3388821542

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

ID	Refine TLS-ID	Selection details	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 3 through 24 )	3 - 24	1 - 22
2	2	chain 'A' and (resid 25 through 75 )	25 - 75	23 - 73
3	3	chain 'A' and (resid 76 through 156 )	76 - 156	74 - 154
4	4	chain 'A' and (resid 157 through 197 )	157 - 197	155 - 195
5	5	chain 'A' and (resid 198 through 217 )	198 - 217	196 - 213
6	6	chain 'A' and (resid 218 through 286 )	218 - 286	214 - 282

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