PDB-5mpw: Crystal structure of Arabidopsis thaliana RNA editing factor MORF1

ID or keywords:

Entry

Database: PDB / ID: 5mpw

Title

Crystal structure of Arabidopsis thaliana RNA editing factor MORF1

Components

Multiple organellar RNA editing factor 1, mitochondrial

Keywords

PLANT PROTEIN / NFLD-related fold

Function / homology

Function and homology information

chloroplast RNA modification / mitochondrial RNA modification / cytidine to uridine editing / chloroplast / mRNA processing / protein dimerization activity / mitochondrion
Similarity search - Function

Biological species

Arabidopsis thaliana (thale cress)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.499 Å

Authors

Haag, S. / Schindler, M. / Berndt, L. / Brennicke, A. / Takenaka, M. / Weber, G.

Citation

Journal: Nucleic Acids Res. / Year: 2017
Title: Crystal structures of the Arabidopsis thaliana organellar RNA editing factors MORF1 and MORF9.
Authors: Haag, S. / Schindler, M. / Berndt, L. / Brennicke, A. / Takenaka, M. / Weber, G.

History

Deposition	Dec 19, 2016	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 22, 2017	Provider: repository / Type: Initial release
Revision 1.1	Mar 1, 2017	Group: Database references
Revision 1.2	May 17, 2017	Group: Database references
Revision 1.3	Dec 27, 2017	Group: Structure summary / Category: entity / struct_keywords / Item: _entity.details / _struct_keywords.text
Revision 1.4	Nov 20, 2024	Group: Data collection / Database references / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5mpw.cif.gz	210.8 KB	Display	PDBx/mmCIF format
PDB format	pdb5mpw.ent.gz	169.7 KB	Display	PDB format
PDBx/mmJSON format	5mpw.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5mpw_validation.pdf.gz	468.5 KB	Display	wwPDB validaton report
Full document	5mpw_full_validation.pdf.gz	474.2 KB	Display
Data in XML	5mpw_validation.xml.gz	25.1 KB	Display
Data in CIF	5mpw_validation.cif.gz	36.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mp/5mpw ftp://data.pdbj.org/pub/pdb/validation_reports/mp/5mpw	HTTPS FTP

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Related structure data

Related structure data	5mpxC 5mpyC C: citing same article (ref.)
Similar structure data	5mpx-d 5m1t-d 2h31-d 5ntk-d 1djg-1 1qas-1 5wi3-d 3go6-d 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	#122 - Feb 2010 Enhanceosome similarity (1) #220 - Apr 2018 Dehalogenases similarity (1) #142 - Oct 2011 PDB Pioneers similarity (1)

Deposited unit

A: Multiple organellar RNA editing factor 1, mitochondrial

B: Multiple organellar RNA editing factor 1, mitochondrial

C: Multiple organellar RNA editing factor 1, mitochondrial

D: Multiple organellar RNA editing factor 1, mitochondrial

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	39.280, 44.940, 68.200
Angle α, β, γ (deg.)	98.100, 91.980, 111.960
Int Tables number	1
Space group name H-M	P1

#1: Protein	Multiple organellar RNA editing factor 1, mitochondrial / RNA editing-interacting protein 8 Mass: 13017.480 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: MORF1, RIP8, At4g20020 / Production host: Escherichia coli (E. coli) / References: UniProt: O49429
#2: Chemical	... ChemComp-BR / BROMIDE ION Mass: 79.904 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: Br
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 474 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	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: 2.11 Å³/Da / Density % sol: 41.8 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion / Details: 0.1 M Tris, pH 8.0 2.8 M NH4SO4

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.916 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 22, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.916 Å / Relative weight: 1
Reflection	Resolution: 1.499→50 Å / Num. obs: 66951 / % possible obs: 97.6 % / Redundancy: 6.5 % / R_sym value: 0.11 / Net I/σ(I): 10.3
Reflection shell	Resolution: 1.5→1.54 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 1.5 / Num. unique all: 4771 / CC_1/2: 0.563 / R_sym value: 0.79 / % possible all: 94

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Processing

Software

Name	Version	Classification
PHENIX	1.10.1_2155	refinement
PDB_EXTRACT	3.22	data extraction
XDS		data reduction
XSCALE		data scaling
autoSHARP		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.499→37.982 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 17.91

	R_factor	Num. reflection	% reflection
R_free	0.1923	3348	5 %
R_work	0.1573	-	-
obs	0.1591	66950	97.83 %

Solvent computation

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

Displacement parameters

B_iso max: 109.69 Å² / B_iso mean: 22.2694 Å² / B_iso min: 5.99 Å²

Refinement step

Cycle: final / Resolution: 1.499→37.982 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3633	0	46	474	4153
B_iso mean	-	-	40.72	31.05	-
Num. residues	-	-	-	-	459

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.013	3826
X-RAY DIFFRACTION	f_angle_d	1.24	5187
X-RAY DIFFRACTION	f_chiral_restr	0.102	538
X-RAY DIFFRACTION	f_plane_restr	0.008	683
X-RAY DIFFRACTION	f_dihedral_angle_d	19.004	1440

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 24

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.4989-1.5204	0.2413	135	0.2389	2572	2707	94
1.5204-1.5431	0.2563	135	0.2199	2553	2688	96
1.5431-1.5672	0.2426	136	0.2179	2592	2728	95
1.5672-1.5929	0.2553	137	0.205	2594	2731	96
1.5929-1.6203	0.2279	140	0.1974	2671	2811	97
1.6203-1.6498	0.2454	136	0.1836	2590	2726	97
1.6498-1.6815	0.2336	139	0.1795	2627	2766	97
1.6815-1.7158	0.2262	139	0.1696	2653	2792	97
1.7158-1.7532	0.1946	139	0.1679	2627	2766	97
1.7532-1.7939	0.1904	141	0.1622	2687	2828	98
1.7939-1.8388	0.1915	137	0.1592	2600	2737	98
1.8388-1.8885	0.1895	141	0.1539	2690	2831	98
1.8885-1.9441	0.1894	141	0.154	2667	2808	98
1.9441-2.0068	0.1956	139	0.1508	2635	2774	98
2.0068-2.0785	0.1849	140	0.1441	2659	2799	98
2.0785-2.1618	0.1897	141	0.1467	2679	2820	98
2.1618-2.2601	0.1707	140	0.1425	2677	2817	99
2.2601-2.3793	0.1749	140	0.1558	2660	2800	99
2.3793-2.5283	0.1893	142	0.1632	2689	2831	99
2.5283-2.7235	0.198	141	0.1696	2671	2812	99
2.7235-2.9975	0.1773	143	0.1664	2724	2867	99
2.9975-3.4309	0.1913	141	0.1515	2672	2813	100
3.4309-4.3217	0.1569	142	0.1215	2709	2851	100
4.3217-37.9946	0.2012	143	0.1488	2704	2847	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	0.7718	0.5956	1.32	0.4057	1.003	2.3185	0.1019	-0.0506	-0.0265	0.1174	0.0076	0.0453	-0.0449	0.2342	-0.0831	0.1367	-0.01	0.0155	0.1556	-0.0165	0.1113	18.6321	-0.5212	55.1561
2	2.5091	-0.0696	0.182	2.3056	-0.3101	3.1065	-0.0076	-0.1444	0.2898	0.1595	0.074	0.2598	-0.1183	-0.1768	-0.0106	0.0822	-0.0043	0.0201	0.0697	-0.0029	0.1117	12.7738	10.6264	84.1727
3	3.8421	-0.2341	0.208	3.2787	0.7371	2.7286	0.0613	0.234	0.081	-0.2219	0.0232	0.0941	0.1835	0.0103	-0.0707	0.0851	-0.0315	0.0086	0.0714	0.0333	0.0672	19.2669	8.6525	75.4305
4	2.1148	2.676	-0.1344	4.7054	0.0005	2.0154	0.012	-0.4922	-0.3234	-0.0612	-0.0805	-0.401	0.0662	0.2798	0.0326	0.1052	0.0038	-0.0038	0.1723	0.0414	0.1141	21.2337	2.3852	89.7919
5	8.0174	-5.8129	-7.1428	6.5825	7.5873	9.2636	0.1447	-0.1246	0.0565	0.1176	-0.1843	-0.0502	-0.1593	-0.1523	-0.0699	0.1287	-0.0227	-0.0372	0.123	0.012	0.1692	31.4756	9.966	52.8864
6	3.4179	-0.4284	-0.5267	3.2037	1.2444	3.354	0.0611	-0.5961	-0.1377	0.6933	0.1034	-0.1948	-0.0136	0.4056	-0.1886	0.2199	-0.0353	-0.0238	0.1687	0.0283	0.1144	29.0889	23.3329	83.2609
7	5.4507	-1.2007	-3.3819	5.8174	4.2984	7.28	0.1301	-0.4979	0.1462	0.0838	0.0193	-0.2179	-0.2383	0.5851	-0.1658	0.0885	-0.0585	-0.0099	0.1494	0.015	0.1053	33.3095	29.5293	79.138
8	3.9298	0.7006	0.1207	2.5563	0.433	0.7687	0.0441	-0.0916	0.1197	-0.194	0.0013	-0.0994	-0.2736	0.3726	0.0012	0.1002	-0.0372	0.0066	0.0998	-0.0129	0.0936	29.9249	28.6457	72.2646
9	5.9315	0.4457	4.2749	3.8352	-0.6089	5.5628	0.2004	0.1412	-0.7	-0.1983	0.1788	-0.7362	0.7102	0.8035	-0.1809	0.1258	0.034	0.0507	0.1771	-0.0304	0.3286	36.3446	16.4891	69.5488
10	3.1655	0.4551	0.5111	1.9371	-0.3869	3.8925	-0.0106	0.0533	-0.0617	-0.078	0.0395	0.0729	-0.0909	-0.2478	-0.0173	0.0497	-0.0177	0.017	0.0542	-0.008	0.0754	21.2396	23.4193	70.1951
11	3.4319	3.524	1.97	6.006	3.0511	5.8412	0.0192	-0.089	0.7838	-0.3239	-0.0913	0.2875	-0.5956	-0.0985	-0	0.1908	-0.0049	-0.0266	0.0824	-0.0013	0.2256	23.458	36.4121	73.111
12	0.766	-1.4625	-0.6871	5.182	2.2577	0.9412	0.1732	0.0413	-0.015	-0.1484	-0.3279	-0.0369	0.1759	-0.212	0.1034	0.1396	0.0031	0.0194	0.145	0.0147	0.1331	29.5943	7.2348	70.7693
13	3.0231	0.0375	0.2152	2.7725	0.1415	1.9485	0.0557	0.2384	-0.0905	-0.3049	-0.0668	-0.1843	0.1505	0.2949	0.0123	0.1055	0.0391	0.0175	0.117	-0.0024	0.0725	36.251	-9.096	45.844
14	3.5923	-0.5152	0.1072	3.3969	-0.2731	3.896	0.0465	-0.3726	0.0802	0.2592	-0.0038	0.0519	-0.0838	-0.1294	-0.0474	0.0651	0.032	-0.0184	0.1087	-0.0028	0.0742	29.6535	-3.4407	52.5365
15	4.8083	-3.363	4.6182	7.2457	0.0088	7.6926	0.2014	-0.289	-0.4465	-0.4624	-0.0923	0.4683	0.4055	-0.5773	-0.1837	0.1635	-0.0161	-0.0113	0.1084	0.0189	0.1862	28.3656	-18.7491	47.9984
16	4.764	-1.3888	-5.9053	0.4408	1.8993	7.7988	0.0089	-0.1978	0.0568	-0.0196	0.1859	-0.015	0.1214	0.2805	-0.146	0.1748	-0.0021	-0.042	0.1385	0.0029	0.2	16.7276	17.0759	65.2748
17	3.2857	0.0156	-0.7456	0.787	-1.2724	2.1178	0.1229	0.4837	-0.5219	-0.5029	-0.1433	-0.0217	0.4839	-0.3208	-0.0289	0.2759	0.0422	-0.0239	0.1589	-0.06	0.1468	19.7521	-0.6309	35.8747
18	2.6539	-0.1974	0.0735	2.5461	0.2364	2.9432	0.0846	0.1629	0.0791	-0.1986	-0.0697	0.0408	-0.2448	-0.1402	-0.0081	0.0946	0.0349	-0.0011	0.0895	0.0122	0.0655	19.7641	9.0933	40.6761
19	2.8847	0.5942	2.8511	8.0977	0.1992	2.97	-0.1192	-0.0886	0.103	0.3153	0.0596	-0.0461	-0.4665	0.2553	0.0912	0.1797	0.0383	0.0112	0.2083	0.0313	0.0997	26.4002	15.3199	32.0963

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 76 through 88 )	A	76 - 88
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 89 through 147 )	A	89 - 147
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 148 through 179 )	A	148 - 179
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 180 through 190 )	A	180 - 190
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 76 through 88 )	B	76 - 88
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 89 through 104 )	B	89 - 104
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 105 through 120 )	B	105 - 120
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 121 through 147 )	B	121 - 147
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 148 through 156 )	B	148 - 156
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 157 through 179 )	B	157 - 179
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 180 through 189 )	B	180 - 189
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 76 through 88 )	C	76 - 88
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 89 through 147 )	C	89 - 147
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 148 through 179 )	C	148 - 179
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 180 through 190 )	C	180 - 190
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 76 through 88 )	D	76 - 88
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 89 through 104 )	D	89 - 104
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 105 through 179 )	D	105 - 179
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 180 through 190 )	D	180 - 190

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