PDB-6pgl: Structure of Kluyveromyces marxianus Usb1 with uridine monophosphate

ID or keywords:

Entry

Database: PDB / ID: 6pgl

Title

Structure of Kluyveromyces marxianus Usb1 with uridine monophosphate

Components

Uncharacterized protein YLR132C

Keywords

HYDROLASE /

exonuclease /

U6 snRNA / 2H phosphodiesterase superfamily

Function / homology

Function and homology information

U6 snRNA 3'-end processing /

nuclease activity /

lyase activity /

nucleus
Similarity search - Function

Biological species

Kluyveromyces marxianus (yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.845 Å

Authors

Nomura, Y. / Montemayor, E.J. / Butcher, S.E.

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	R01 GM065166	United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	R35 GM118131	United States

Citation

Journal: Nucleic Acids Res. / Year: 2020
Title: Structural basis for the evolution of cyclic phosphodiesterase activity in the U6 snRNA exoribonuclease Usb1.
Authors: Nomura, Y. / Montemayor, E.J. / Virta, J.M. / Hayes, S.M. / Butcher, S.E.

History

Deposition	Jun 24, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 11, 2019	Provider: repository / Type: Initial release
Revision 1.1	May 20, 2020	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Mar 13, 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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PDBx/mmCIF format	6pgl.cif.gz	271.4 KB	Display	PDBx/mmCIF format
PDB format	pdb6pgl.ent.gz	217.2 KB	Display	PDB format
PDBx/mmJSON format	6pgl.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

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

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Related structure data

Related structure data	6pfqC C: citing same article (ref.)
Similar structure data	1ojq-d 1wr2-d 6pfq-2 2bsh-d 6p7f-d 4u02-3 5v1v-d 1p1o-d 6d34-d 4f9t-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) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

6pfqC

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#222 - Jun 2018 Proteins and Nanoparticles similarity (1) #254 - Feb 2021 Cellulose Synthase similarity (1) #86 - Feb 2007 Exosomes similarity (1)

Deposited unit

A: Uncharacterized protein YLR132C

B: Uncharacterized protein YLR132C

C: Uncharacterized protein YLR132C

hetero molecules

76.4 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Uncharacterized protein YLR132C

hetero molecules

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

2

B: Uncharacterized protein YLR132C

hetero molecules

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

3

C: Uncharacterized protein YLR132C

hetero molecules

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

Unit cell

Length a, b, c (Å)	69.957, 110.344, 114.697
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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Protein , 1 types, 3 molecules ABC

#1: Protein	Uncharacterized protein YLR132C / U6 snRNA phosphodiesterase Mass: 24478.412 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Kluyveromyces marxianus (strain DMKU3-1042 / BCC 29191 / NBRC 104275) (yeast) Strain: DMKU3-1042 / BCC 29191 / NBRC 104275 / Gene: KLMA_50491 / Production host: Escherichia coli (E. coli) / References: UniProt: W0TCJ5

#1: Protein

Uncharacterized protein YLR132C / U6 snRNA phosphodiesterase

Mass: 24478.412 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Kluyveromyces marxianus (strain DMKU3-1042 / BCC 29191 / NBRC 104275) (yeast)
Strain: DMKU3-1042 / BCC 29191 / NBRC 104275 / Gene: KLMA_50491 / Production host:

Escherichia coli (E. coli) / References: UniProt: W0TCJ5

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Non-polymers , 7 types, 438 molecules

#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-U5P / URIDINE-5'-MONOPHOSPHATE / Uridine monophosphate Mass: 324.181 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₉H₁₃N₂O₉P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol Mass: 150.173 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#5: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₂H₆O₂
#6: Chemical	ChemComp-PG6 / 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE / Polyethylene glycol Mass: 266.331 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₂H₂₆O₆
#7: Chemical	ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₈O₅ / Comment: precipitant*YM
#8: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 419 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.01 Å³/Da / Density % sol: 59.19 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 1.2 M potassium sodium tartrate, 100 mM HEPES, 30% glycerol

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
Detector	Type: RAYONIX MX-300 / Detector: CCD / Date: Feb 17, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9787 Å / Relative weight: 1
Reflection	Resolution: 1.84→79.52 Å / Num. obs: 82782 / % possible obs: 94.9 % / Redundancy: 8.2 % / Net I/σ(I): 15.3
Reflection shell	Resolution: 1.84→2.04 Å / Num. unique obs: 2827

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Processing

Software

Name	Version	Classification
PHENIX	(1.14_3260: ???)	refinement
STARANISO		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.845→55.172 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.9 / Phase error: 26.27

	R_factor	Num. reflection	% reflection
R_free	0.2194	3843	3.64 %
R_work	0.1883	-	-
obs	0.1894	105619	71.51 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.845→55.172 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4771	0	198	419	5388

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	5074
X-RAY DIFFRACTION	f_angle_d	0.987	6854
X-RAY DIFFRACTION	f_dihedral_angle_d	6.835	4123
X-RAY DIFFRACTION	f_chiral_restr	0.057	806
X-RAY DIFFRACTION	f_plane_restr	0.006	869

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 (%)
1.8446-1.868	0.5194	6	0.4415	91	X-RAY DIFFRACTION	2
1.868-1.8925	0.3406	2	0.3347	183	X-RAY DIFFRACTION	3
1.8925-1.9185	0.483	5	0.3354	194	X-RAY DIFFRACTION	4
1.9185-1.9459	0.3734	10	0.3129	387	X-RAY DIFFRACTION	7
1.9459-1.9749	0.3845	21	0.296	603	X-RAY DIFFRACTION	12
1.9749-2.0058	0.3628	46	0.2736	1195	X-RAY DIFFRACTION	23
2.0058-2.0387	0.2519	75	0.2846	1627	X-RAY DIFFRACTION	31
2.0387-2.0738	0.2875	81	0.2663	2060	X-RAY DIFFRACTION	39
2.0738-2.1115	0.2815	114	0.2615	2761	X-RAY DIFFRACTION	53
2.1115-2.1522	0.2859	144	0.2674	3868	X-RAY DIFFRACTION	73
2.1522-2.1961	0.3006	176	0.2667	4690	X-RAY DIFFRACTION	89
2.1961-2.2438	0.3128	189	0.2569	5069	X-RAY DIFFRACTION	96
2.2438-2.296	0.2748	184	0.2495	5274	X-RAY DIFFRACTION	100
2.296-2.3535	0.2634	194	0.2378	5271	X-RAY DIFFRACTION	100
2.3535-2.4171	0.2736	210	0.2237	5302	X-RAY DIFFRACTION	100
2.4171-2.4882	0.2564	200	0.213	5263	X-RAY DIFFRACTION	100
2.4882-2.5685	0.2518	191	0.2113	5245	X-RAY DIFFRACTION	100
2.5685-2.6603	0.2353	197	0.2043	5292	X-RAY DIFFRACTION	100
2.6603-2.7668	0.2325	203	0.1965	5225	X-RAY DIFFRACTION	100
2.7668-2.8928	0.238	209	0.194	5294	X-RAY DIFFRACTION	100
2.8928-3.0453	0.2202	191	0.1867	5281	X-RAY DIFFRACTION	100
3.0453-3.236	0.2226	196	0.1739	5255	X-RAY DIFFRACTION	100
3.236-3.4859	0.1908	205	0.1722	5278	X-RAY DIFFRACTION	100
3.4859-3.8366	0.1674	186	0.156	5294	X-RAY DIFFRACTION	100
3.8366-4.3915	0.1957	200	0.1415	5268	X-RAY DIFFRACTION	100
4.3915-5.5321	0.198	205	0.1513	5249	X-RAY DIFFRACTION	100
5.5321-55.1967	0.1817	203	0.1883	5257	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	0.7014	-0.2366	0.4835	0.2082	0.029	0.572	-0.0671	-0.1925	-0.0873	0.0129	0.0017	-0.0591	0.0737	0.0345	-0	0.2029	-0.0208	0.026	0.2196	-0.01	0.179	-23.7087	-27.6226	-2.0303
2	1.1505	0.0377	-0.1494	0.0586	-0.1026	0.8178	0.0347	0.0752	0.2324	0.0041	-0.015	-0.0531	-0.0734	0.0282	-0	0.1693	-0.0061	0.0265	0.1609	0.0256	0.2508	-17.5557	-13.7312	-8.8639
3	1.0494	-0.1533	-0.1641	0.6648	-0.1853	0.4716	0.0563	0.0015	0.0178	0.0064	-0.0282	0.0823	-0.032	-0.0027	0	0.1848	0.0147	-0.0005	0.2293	0.001	0.1619	-27.1186	-22.6695	-6.9653
4	0.6846	0.4431	0.2026	1.2344	0.9244	1.0876	-0.0729	0.0677	-0.223	-0.2794	0.1206	-0.3206	-0.0441	0.33	-0.0051	0.2725	-0.0515	0.0209	0.317	-0.0624	0.2322	-6.311	-38.0781	-29.5799
5	0.3972	0.2973	-0.1528	0.4424	0.4722	0.2256	-0.0914	0.0482	0.0197	-0.3003	-0.0143	0.1006	-0.1748	0.0194	-0.0214	0.3352	-0.0039	-0.0631	0.2488	-0.0465	0.197	-14.9976	-33.0422	-31.9265
6	0.1836	-0.0182	-0.0904	0.2033	0.108	0.2351	-0.1215	0.1688	-0.0898	-0.1019	-0.0091	0.1581	0.0799	-0.0894	-0.1666	0.2702	-0.0319	-0.0214	0.2805	-0.1077	0.2545	-17.8277	-45.2916	-28.6877
7	0.077	-0.0205	-0.0644	0.1313	-0.0181	0.0353	0.0413	-0.3741	0.1475	0.2078	-0.3803	0.3399	-0.0337	-0.5791	-0.0481	0.3221	-0.0736	0.0603	0.3689	-0.1263	0.2871	-24.6816	-48.3277	-20.9429
8	0.0146	-0.0103	-0.0262	0.0202	0.0133	0.0112	0.056	-0.1954	0.0937	0.1413	-0.1779	0.097	0.0504	0.0385	0.0001	0.3178	-0.0427	-0.0389	0.3925	-0.0572	0.2331	-9.0801	-39.3709	-11.5862
9	0.4469	-0.1186	0.1852	0.5412	-0.2027	0.1599	-0.1686	-0.0135	-0.5365	-0.1865	0.5805	-0.4952	-0.3019	0.4541	0.3249	0.365	-0.2914	0.132	0.4634	-0.3514	0.2757	0.1251	-29.9762	-33.3678
10	0.2061	0.0003	0.2237	0.8679	-0.4178	0.5396	0.052	-0.0279	0.0212	-0.4736	0.1439	-0.0019	-0.1178	-0.1104	0.0627	0.3008	-0.0378	-0.0034	0.2063	0.0241	0.2738	-19.0051	-49.5282	4.0705
11	0.6144	0.8648	-0.249	0.8062	-0.2221	0.5605	-0.0836	-0.2419	-0.155	-0.825	0.0361	-0.1143	-0.3762	-0.1343	-0.1707	0.3138	-0.0335	0.0365	0.025	0.0847	0.2322	-13.0162	-48.1422	4.1667
12	0.0026	-0.0019	0.0488	0.026	-0.0894	0.3699	0.1333	0.0933	-0.3039	-0.3081	-0.1404	-0.0505	0.3197	0.6969	-0.0807	0.9091	-0.0857	0.4054	0.4313	-0.1793	1.0143	-0.1217	-68.4539	-5.0738
13	0.2219	0.021	0.1042	0.0031	-0.0729	0.1468	0.0808	-0.1645	-0.0814	-0.0149	-0.084	-0.065	0.0747	-0.0327	0.0102	0.2087	-0.016	-0.001	0.1654	0.0662	0.244	-13.5358	-55.4668	10.014
14	0.1079	-0.0842	-0.0087	0.1601	0.1508	0.1075	-0.1496	-0.2728	-0.3576	0.1314	-0.0093	-1.0114	0.3075	0.1479	-0.0855	0.3069	0.2261	0.1628	-0.8836	0.339	0.7056	-8.8685	-69.3119	7.0877
15	0.035	0.1174	-0.0287	0.0494	-0.0255	0.2186	0.0048	-0.3623	-0.2811	-0.2725	-0.0234	-0.3027	-0.1865	0.0599	-0.0495	0.1948	-0.0667	0.0097	0.256	0.1098	0.3318	-6.7089	-50.0729	12.0353
16	0.3907	0.1457	-0.3736	1.1373	-0.7218	0.3733	-0.1679	-0.1164	-0.122	-0.2783	0.0526	0.0707	-0.0846	-0.024	-0.1115	0.2521	-0.0506	0.0309	0.2448	0.0493	0.225	-16.3611	-53.6035	9.3315

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 58 through 108 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 109 through 206 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 207 through 275 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 62 through 158 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 159 through 206 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 207 through 225 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 226 through 243 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 244 through 254 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 255 through 275 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 61 through 96 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 97 through 128 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 129 through 145 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 146 through 177 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 178 through 194 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 195 through 225 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 226 through 275 )

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