PDB-3w6s: yeast N-acetyltransferase Mpr1 involved in oxidative stress toler...

ID or keywords:

Entry

Database: PDB / ID: 3w6s

Title

yeast N-acetyltransferase Mpr1 involved in oxidative stress tolerance via proline metabolism

Components

MPR1 protein

Keywords

TRANSFERASE / detoxification of L-azetidine-2-carboxylate / antioxidant enzyme

Function / homology

Function and homology information

L-glutamate-5-semialdehyde N-acetyltransferase / acyltransferase activity, transferring groups other than amino-acyl groups /

mitochondrion
Similarity search - Function

Biological species

Saccharomyces cerevisiae (brewer's yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

Nasuno, R. / Hirano, Y. / Itoh, T. / Hakoshima, T. / Hibi, T. / Takagi, H.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Structural and functional analysis of the yeast N-acetyltransferase Mpr1 involved in oxidative stress tolerance via proline metabolism
Authors: Nasuno, R. / Hirano, Y. / Itoh, T. / Hakoshima, T. / Hibi, T. / Takagi, H.

History

Deposition	Feb 21, 2013	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jul 17, 2013	Provider: repository / Type: Initial release
Revision 1.1	Aug 7, 2013	Group: Database references
Revision 1.2	Nov 8, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3w6s.cif.gz	269.2 KB	Display	PDBx/mmCIF format
PDB format	pdb3w6s.ent.gz	218.4 KB	Display	PDB format
PDBx/mmJSON format	3w6s.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/w6/3w6s ftp://data.pdbj.org/pub/pdb/validation_reports/w6/3w6s	HTTPS FTP

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Related structure data

Related structure data	3w6xC 3w91SC C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4dkb-1 5z5d-d 4rnc-2 3iib-d 3w6x-2 5z5f-d 2wtn-d 4yl5-1 5z5h-d 4fq7-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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#146 - Feb 2012 Aminoglycoside Antibiotics similarity (3) #97 - Jan 2008 Circadian Clock Proteins similarity (3)

Deposited unit

A: MPR1 protein

B: MPR1 protein

C: MPR1 protein

hetero molecules

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

1

A: MPR1 protein

hetero molecules

A: MPR1 protein

hetero molecules

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

2

B: MPR1 protein

C: MPR1 protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	83.862, 83.862, 193.819
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	151
Space group name H-M	P3₁12

Components on special symmetry positions

ID	Model	Components
1	1	A-302- MG

#1: Protein	MPR1 protein Mass: 27942.863 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: sigma1278b / Gene: MPR1 / Plasmid: pQE2 / Production host: Escherichia coli (E. coli) / Strain (production host): SG13009 References: UniProt: E9P8D2, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical	ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol Mass: 282.331 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₁₂H₂₆O₇ / Comment: precipitant*YM
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 228 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.35 Å³/Da / Density % sol: 47.59 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.9793 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 22, 2008
Radiation	Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9793 Å / Relative weight: 1
Reflection twin	Operator: -h,-k,l / Fraction: 0.27
Reflection	Resolution: 1.9→48.3 Å / Num. obs: 61875 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.9 % / B_iso Wilson estimate: 33.5 Å² / R_merge(I) obs: 0.06
Reflection shell	Resolution: 1.9→2 Å / Redundancy: 7.7 % / R_merge(I) obs: 0.287 / Mean I/σ(I) obs: 2.4 / Num. unique all: 8966 / % possible all: 100

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Processing

Software

Name	Version	Classification
ADSC	Quantum	data collection
PHASER		phasing
PHENIX	(phenix.refine: 1.8.1_1168)	refinement
MOSFLM		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3W91

3w91

Resolution: 1.9→48.271 Å / Occupancy max: 1 / Occupancy min: 0.05 / FOM work R set: 0.817 / σ(F): 1.35 / Phase error: 25.7 / Stereochemistry target values: TWIN_LSQ_F

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1872	3088	5 %	random
R_work	0.1657	-	-	-
all	0.1706	61875	-	-
obs	0.1706	61806	99.98 %	-

Solvent computation

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

Displacement parameters

B_iso max: 75.24 Å² / B_iso mean: 30.373 Å² / B_iso min: 9.46 Å²

Refine analyze

Luzzati coordinate error obs: 0.3107 Å

Refinement step

Cycle: LAST / Resolution: 1.9→48.271 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5257	0	43	228	5528

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	5508
X-RAY DIFFRACTION	f_angle_d	1.015	7515
X-RAY DIFFRACTION	f_dihedral_angle_d	13.532	1901
X-RAY DIFFRACTION	f_chiral_restr	0.053	825
X-RAY DIFFRACTION	f_plane_restr	0.004	952

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20 / % reflection obs: 95 %

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work
1.9001-1.9329	0.2551	152	0.2305	2878
1.9329-1.968	0.2502	156	0.2181	2893
1.968-2.0059	0.2448	154	0.2052	2928
2.0059-2.0468	0.228	152	0.2101	2937
2.0468-2.0913	0.1999	154	0.2073	2907
2.0913-2.14	0.198	153	0.2017	2896
2.14-2.1935	0.2358	151	0.1991	2913
2.1935-2.2528	0.2181	149	0.1947	2920
2.2528-2.3191	0.2197	153	0.1974	2927
2.3191-2.3939	0.1842	154	0.2004	2950
2.3939-2.4795	0.2217	151	0.195	2908
2.4795-2.5787	0.1755	155	0.1938	2903
2.5787-2.6961	0.2122	159	0.191	2932
2.6961-2.8382	0.1942	153	0.1878	2920
2.8382-3.016	0.2222	154	0.1811	2962
3.016-3.2487	0.1946	156	0.1748	2934
3.2487-3.5755	0.1602	154	0.1549	2945
3.5755-4.0925	0.1901	161	0.1318	2972
4.0925-5.1545	0.1386	150	0.1117	2993
5.1545-40.9925	0.2132	165	0.1607	3071

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	0.0055	-0.0023	0.0063	0.0056	-0.0057	0.0207	0.0046	-0.0047	-0.0157	0.0456	0.0127	-0.0072	-0.0321	0.0275	0	0.0978	-0.004	0.0003	0.1028	0.0042	0.0969	36.0179	-27.4281	55.7108
2	0.0024	0.0028	0.0014	-0.0002	0	0.0009	0.0043	0.0311	-0.0018	0.0123	-0.013	0.003	0.0016	-0.0209	0	0.0718	-0.0143	0.0051	0.1386	-0.0146	0.0973	23.1814	-31.4314	40.3391
3	-0.0013	0.005	-0.0042	0.0022	-0.001	0.0033	0.0197	0.0706	0.0059	0.0013	0.0115	-0.011	0.0181	-0.0268	0	0.0533	-0.0224	0.0028	0.0369	-0.0026	0.0823	30.6447	-29.6563	39.1668
4	0.0008	0.001	-0.0012	0.0001	-0.0005	0.001	-0.004	-0.0004	0.0025	0.0123	0.0028	0.0051	0.0125	-0.0131	-0	0.1962	0.0028	0.0499	0.1533	0.0027	0.1632	22.0093	-31.3203	58.8341
5	0.0012	-0.0008	0.0052	0.0035	-0.0006	0.0099	-0.0339	0.0006	-0.0062	-0.0231	-0.0139	0.0268	-0.0452	0.0037	0	0.068	-0.0054	0.0111	0.0778	-0.0014	0.0823	36.4174	-24.3927	44.4237
6	-0.0036	-0.0048	-0.0051	0.0042	0.0055	0.006	0.0987	-0.0346	0.0325	-0.0343	0.0381	-0.0026	-0.0752	-0.0307	-0	0.0229	0.1999	0.0628	-0.3157	-0.0448	0.1412	31.9099	-17.4659	45.6932
7	-0.0028	-0.0019	-0.0016	0.0023	-0.0022	-0.0018	0.0139	-0.0133	0.0054	-0.0145	0.0245	-0.017	-0.0244	-0.0005	-0	0.2445	0.1687	0.0673	-0.1702	0.0327	0.1208	32.4332	-8.3384	40.7013
8	0.0009	0.0004	0.001	0.0003	-0.0002	0.0001	-0.0019	0.0067	0.007	-0.0057	-0.0002	0.0003	0.0036	-0.0205	0	0.1314	0.1931	-0.0029	0.1248	0.1009	0.1172	26.7358	-14.2054	24.3828
9	-0.001	-0.0026	0.0018	0.0012	0.0011	0.0001	0.0215	-0.0275	0.0319	-0.0047	-0.0178	-0.0237	-0.005	-0.0148	0	0.1691	-0.005	0.0251	0.0692	-0.0121	0.1526	37.054	-10.2292	49.4161
10	0.0035	-0.0012	-0.0005	-0.0003	-0.0005	-0.0005	-0.061	-0.0294	-0.0009	-0.0061	-0.0616	-0.0131	0.012	0.0497	-0	0.0844	0.2649	0.1594	0.0956	0.0021	0.1879	26.4104	21.2073	17.0022
11	-0.0005	-0.004	-0.0028	0.0018	-0.0028	0.0004	-0.0193	0.0086	0.0196	-0.0032	-0.0448	0.0143	0.0375	0.0035	0	0.3667	0.1825	0.1185	-0.0071	-0.0239	0.1967	13.2347	12.4158	17.4228
12	-0.0031	-0.0068	-0.0076	0.0038	-0.002	-0.0036	0.0022	-0.0106	-0.0086	-0.0032	-0.0197	-0.0053	0.0353	-0.0063	0	0.2932	0.375	0.29	-0.0498	-0.0961	0.0961	12.2799	11.9378	26.0568
13	-0.0009	-0.0056	0.0001	0.0012	0.003	0.0002	-0.0297	0.0025	-0.0245	0.0056	0.0058	-0.0094	0.0278	-0.0049	-0	0.4358	0.2225	0.2009	0.0986	-0.0305	0.1455	18.0788	10.9291	10.4702
14	-0.0006	-0.0013	0.0017	0	-0	0.0003	0.0019	-0.0088	0.0001	-0.0014	0.0023	0.0006	0.0111	0.0157	0	0.2521	0.2151	0.0725	0.2893	0.0817	0.2212	24.6771	20.8064	34.7551
15	-0.0007	-0.0009	0.0008	0.0008	-0.0002	-0.0003	-0.0049	0.0146	-0.0022	-0.0039	0.0165	0.0001	0.0053	-0.0164	0	0.3041	0.0962	0.0691	0.1251	0.0535	0.2393	20.5237	1.0679	17.8618
16	-0.0003	-0	0.0004	0.0009	0.0003	-0.0001	0.001	-0.0075	-0.0042	-0.0009	0	-0.0036	0.0147	0.0124	-0	0.296	0.2611	0.1034	0.2322	0.0635	0.2554	29.7598	12.4138	20.745
17	0.0007	-0.0013	-0.0019	0.0007	-0.002	-0.0027	-0.0068	-0.0057	0.0034	0.0113	-0.0034	-0.0047	0.0322	0.0184	0	0.3056	0.1642	0.1089	0.2616	0.0763	0.2919	25.9332	9.3937	33.0814
18	0.0002	-0.0098	-0.0009	0.0061	-0.0036	-0.003	0.0002	0.0075	-0.015	0.0029	0.0066	-0.0042	0.0147	0.0005	-0	0.4428	0.3422	0.148	0.197	0.136	0.3262	25.1277	0.5764	35.5826
19	-0.0003	-0.0027	-0.0005	0.0023	0.0003	-0.0005	-0.0059	0.0105	-0.0036	0.0078	-0.0088	-0.0023	0.0028	0.0027	-0	0.2923	0.1356	0.0873	0.2657	0.0449	0.2985	34.8965	10.6845	27.6737
20	-0.0052	-0.0019	0.0044	0.0067	-0.0097	0.0008	-0.0421	-0.0382	0.0017	-0.0396	-0.0091	-0.0288	0.0463	0.0377	-0	0.4527	0.1985	0.1121	0.0795	0.2005	0.1115	6.1852	13.4743	60.0195
21	0.0005	-0.0024	-0.0003	0.0002	0.0012	0.0006	-0.0182	-0.0017	0.0007	-0.0152	0.0133	0.0075	0.0189	0.0099	0	0.2739	0.0877	0.0267	0.176	0.0265	0.2012	3.7584	22.0453	59.4536
22	0.0004	0.0002	-0.0011	0.0012	0.0003	0.0013	-0.004	0.0047	0.0014	-0.0013	0.0057	-0.0115	-0.0074	0.0115	-0	0.216	0.0644	0.0151	0.1849	0.0233	0.175	12.8818	32.6132	52.7102
23	0.0014	-0.0123	0.0019	-0.0017	-0.0016	0.0005	-0.0396	0.0023	-0.0124	0.0104	-0.0115	-0.0386	0.0171	0.0255	-0	0.1523	0.3929	0.0786	0.0356	0.0118	0.1443	10.5564	26.7883	54.5293
24	-0.0053	-0.0061	0.0041	0.0021	-0.0061	0.0049	-0.064	-0.0357	-0.0185	-0.0181	-0.0642	-0.0383	0.0315	0.0204	-0	0.2769	0.398	0.0584	0.0057	0.1323	0.1575	13.0617	17.2517	51.3727
25	-0.0009	-0.0012	0.0016	0.0006	-0.0014	0.0013	-0.034	-0.0175	-0	0.0118	-0.0216	-0.0132	0.0173	0.0295	-0	0.3067	0.389	-0.0037	0.2107	0.152	0.1594	17.4042	18.2475	60.2033
26	0.0009	-0.0008	0.0002	-0.0001	-0.0017	-0.003	-0.0019	-0.0073	-0.0042	0.0099	0.0259	0.0037	0.0107	0.0283	-0	0.2956	0.1638	0.0204	0.2568	0.0587	0.2482	23.2913	14.4507	50.1708
27	0.0001	-0.0027	0.0007	0.0002	-0.0004	0.0002	0.0067	-0.0056	-0.0133	-0.004	-0.0023	-0.0069	0.0014	-0.0022	0	0.3009	0.2129	-0.0148	0.3619	0.0837	0.3089	28.6788	12.0385	53.926
28	0.0003	-0.0004	0.0005	0.0013	0.0003	-0.0005	-0.0028	-0.0051	-0.0001	0.0001	-0.0035	-0.0029	-0.0025	0.0043	0	0.2638	0.0749	-0.0014	0.3675	0.0359	0.3035	34.0986	25.6262	42.3263
29	0.0008	-0.006	-0.0024	0.0016	-0.0016	-0.001	0.0172	-0.0075	-0.0148	0.0107	-0.0097	-0.0154	0.0158	0.0028	-0	0.331	0.2035	0.0614	0.2637	0.0859	0.2785	22.1174	8.0249	58.5512

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 5:54 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 55:71 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 72:99 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resseq 100:111 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resseq 112:133 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resseq 134:179 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resseq 180:196 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resseq 197:210 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resseq 211:229 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resseq 5:40 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resseq 41:71 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resseq 72:99 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resseq 100:122 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resseq 123:137 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resseq 138:148 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resseq 149:164 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resseq 165:179 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resseq 180:210 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resseq 211:228 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resseq 5:40 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resseq 41:54 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resseq 55:71 )
23	X-RAY DIFFRACTION	23	chain 'C' and (resseq 72:111 )
24	X-RAY DIFFRACTION	24	chain 'C' and (resseq 112:133 )
25	X-RAY DIFFRACTION	25	chain 'C' and (resseq 134:164 )
26	X-RAY DIFFRACTION	26	chain 'C' and (resseq 165:180 )
27	X-RAY DIFFRACTION	27	chain 'C' and (resseq 181:196 )
28	X-RAY DIFFRACTION	28	chain 'C' and (resseq 197:210 )
29	X-RAY DIFFRACTION	29	chain 'C' and (resseq 211:228 )

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-Yorodumi

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Movie

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Structure viewers

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Viewer log

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This page

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This web site

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Options

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Open data

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Basic information

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Structure visualization

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Download

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Validation report

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Related structure data

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Links

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Assembly

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Components

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Processing

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About Yorodumi

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News

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

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Aug 12, 2020. Covid-19 info

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Mar 5, 2020. Novel coronavirus structure data

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

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Jul 12, 2017. Major update of PDB

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Yorodumi