PDB-4oah: Crystal structure of the cytosolic domain of mouse MiD51 H201A mutant

ID or keywords:

Entry

Database: PDB / ID: 4oah

Title

Crystal structure of the cytosolic domain of mouse MiD51 H201A mutant

Components

Mitochondrial dynamic protein MID51

Keywords

TRANSFERASE / nucleotidyl transferase fold

Function / homology

Function and homology information

mitochondrial fission / positive regulation of mitochondrial fission / positive regulation of protein targeting to membrane /

ADP binding / GDP binding / cellular response to hypoxia / mitochondrial outer membrane /

mitochondrion / identical protein binding
Similarity search - Function

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2 Å

Authors

Loson, O.C. / Kaiser, J.T. / Chan, D.C.

Citation

Journal: Structure / Year: 2014
Title: The Mitochondrial Fission Receptor MiD51 Requires ADP as a Cofactor.
Authors: Loson, O.C. / Liu, R. / Rome, M.E. / Meng, S. / Kaiser, J.T. / Shan, S.O. / Chan, D.C.

History

Deposition	Jan 4, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 22, 2014	Provider: repository / Type: Initial release
Revision 1.1	Mar 26, 2014	Group: Database references
Revision 1.2	Feb 28, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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	4oah.cif.gz	541.3 KB	Display	PDBx/mmCIF format
PDB format	pdb4oah.ent.gz	448.2 KB	Display	PDB format
PDBx/mmJSON format	4oah.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/oa/4oah ftp://data.pdbj.org/pub/pdb/validation_reports/oa/4oah	HTTPS FTP

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Related structure data

Related structure data	4oafC 4oagC 4oaiC C: citing same article (ref.)
Similar structure data	4oaf-1 4oaf-2 5ays-d 4nxv-5 4nxv-6 3wdh-d 3cii-1 4i18-1 4edw-d 6xwb-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

Deposited unit

A: Mitochondrial dynamic protein MID51

B: Mitochondrial dynamic protein MID51

C: Mitochondrial dynamic protein MID51

D: Mitochondrial dynamic protein MID51

hetero molecules

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

1

A: Mitochondrial dynamic protein MID51

C: Mitochondrial dynamic protein MID51

hetero molecules

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

2

B: Mitochondrial dynamic protein MID51

D: Mitochondrial dynamic protein MID51

hetero molecules

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

Unit cell

Length a, b, c (Å)	82.434, 79.151, 103.449
Angle α, β, γ (deg.)	90.00, 98.04, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Mitochondrial dynamic protein MID51 / Mitochondrial dynamic protein of 51 kDa homolog / Mitochondrial elongation factor 1 / Smith-Magenis ...Mitochondrial dynamic protein of 51 kDa homolog / Mitochondrial elongation factor 1 / Smith-Magenis syndrome chromosomal region candidate gene 7 protein-like Mass: 37185.680 Da / Num. of mol.: 4 / Fragment: Cytosolic domain, unp residues 134-463 / Mutation: H201A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mid51, MiD51 (aka SMCR7L), Mief1, Smcr7l / Plasmid: pGEX6P1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8BGV8
#2: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1157 / 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: 2.25 Å³/Da / Density % sol: 45.25 %
Crystal grow	Temperature: 296.15 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 100 mM Bis-Tris pH 6.5, 200 mM lithium sulfate, 25% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 296.15K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

SSRL

/ Beamline: BL12-2 / Wavelength: 1.03 Å

Detector

Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 26, 2013 / Details: K-B focusing mirrors

Radiation

Monochromator: Liquid nitrogen-cooled double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.03 Å / Relative weight: 1

Reflection

Resolution: 1.85→39.58 Å / Num. all: 340884 / Num. obs: 106662 / % possible obs: 95.5 %

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	R_sym value	Diffraction-ID	% possible all
1.85-1.95	2.9	0.978	0.8	0.978	1	80.1
1.95-2.07	3.3	0.611	1.3	0.611	1	98.9
2.07-2.22	3.2	0.354	2.2	0.354	1	97.1
2.22-2.39	3.3	0.23	3.3	0.23	1	98.6
2.39-2.62	3.2	0.149	5.2	0.149	1	98.4
2.62-2.93	3.2	0.096	8	0.096	1	98
2.93-3.38	3.3	0.054	13.6	13.6	1	98.7
3.38-4.15	3.2	0.034	19.5	0.034	1	98.1
4.15-5.86	3.2	0.027	22.2	0.027	1	97.5
5.86-36.326	3.2	0.024	20.3	0.024	1	97.1

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

	Highest resolution	Lowest resolution
Rotation	4.29 Å	36.33 Å
Translation	4.29 Å	36.33 Å

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Processing

Software

Name	Version	Classification
SCALA		data scaling
PHASER	2.5.2	phasing
PHENIX	1.8.1_1168	refinement
PDB_EXTRACT	3.14	data extraction
XSCALE		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2→31.506 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.22 / σ(F): 1.34 / Phase error: 23.99 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2169	1639	1.88 %
R_work	0.172	-	-
obs	0.1728	87268	97.92 %

Solvent computation

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

Displacement parameters

B_iso mean: 30.9963 Å²

Refinement step

Cycle: LAST / Resolution: 2→31.506 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10246	0	30	1157	11433

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	10491
X-RAY DIFFRACTION	f_angle_d	1.205	14326
X-RAY DIFFRACTION	f_dihedral_angle_d	13.082	3866
X-RAY DIFFRACTION	f_chiral_restr	0.076	1666
X-RAY DIFFRACTION	f_plane_restr	0.006	1844

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 (%)
2-2.0588	0.279	137	0.2543	7148	X-RAY DIFFRACTION	99
2.0588-2.1253	0.2756	136	0.233	7117	X-RAY DIFFRACTION	98
2.1253-2.2012	0.2675	136	0.211	7076	X-RAY DIFFRACTION	97
2.2012-2.2893	0.2335	133	0.1992	6973	X-RAY DIFFRACTION	97
2.2893-2.3935	0.2897	138	0.1934	7182	X-RAY DIFFRACTION	99
2.3935-2.5196	0.2681	137	0.1861	7196	X-RAY DIFFRACTION	99
2.5196-2.6774	0.2217	134	0.1797	7034	X-RAY DIFFRACTION	97
2.6774-2.884	0.2323	137	0.1797	7120	X-RAY DIFFRACTION	98
2.884-3.174	0.2253	139	0.1673	7254	X-RAY DIFFRACTION	99
3.174-3.6327	0.2012	135	0.1545	7077	X-RAY DIFFRACTION	97
3.6327-4.5746	0.1688	139	0.1356	7257	X-RAY DIFFRACTION	99
4.5746-31.5097	0.1968	138	0.1701	7195	X-RAY DIFFRACTION	97

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	0.7146	0.2324	0.7702	1.7545	-1.9908	2.2467	-0.1352	0.0606	-0.0766	-0.879	0.3195	0.082	0.845	-0.3787	-0.0828	0.3571	-0.0179	0.0187	0.1522	-0.0395	0.1519	94.1116	1.1632	129.8273
2	0.3475	0.3015	0.3512	1.2553	-0.1186	0.3545	-0.03	-0.0541	0.0534	0.0141	0.0122	-0.0088	0.0529	0.0138	0.0142	0.1602	0.0278	-0.0029	0.1213	-0.0027	0.122	107.5537	21.7985	132.4342
3	4.1395	2.4798	-0.4701	5.3113	-2.684	3.9576	0.3474	-0.6992	0.5503	0.3672	-0.0904	0.6532	-0.7518	-0.1283	0.1017	0.3607	-0.0413	-0.0572	0.1595	-0.0477	0.1472	119.6807	40.9465	136.3007
4	0.7697	0.733	-0.1961	1.3135	-0.0085	1.2004	-0.0452	0.0466	0.2851	-0.0284	0.0335	0.3923	-0.2132	-0.2529	-0.0155	0.1925	0.0259	-0.0274	0.1521	0.0311	0.1916	100.0465	29.4338	127.0122
5	2.55	0.6679	-0.2042	1.6688	-2.1729	3.3838	0.1232	-0.3107	-0.2684	0.2262	-0.0723	0.7241	-0.3172	-0.8499	0.12	0.1682	0.0402	0.0135	0.3748	-0.0547	0.4541	89.7415	18.1499	127.8408
6	0.3682	-0.0156	-0.0078	1.7323	-0.2452	0.3726	0.0056	-0.0874	-0.0364	0.0393	-0.0129	0.0951	0.1695	-0.0796	0.027	0.2623	-0.025	-0.0171	0.1178	0.0141	0.1463	107.8666	18.8202	140.2977
7	1.5598	0.2073	0.0607	2.0074	-0.529	2.2734	-0.0507	0.1256	0.0113	-0.0648	0.0086	-0.0936	0.0593	0.0519	0.044	0.2244	-0.0148	0.0041	0.1092	0.0215	0.1035	103.6446	0.5919	146.5505
8	1.0337	1.11	-0.6446	4.0248	-0.6031	0.8301	0.1733	-0.1088	0.312	0.7833	-0.1094	1.1555	-0.119	-0.3071	-0.0026	0.313	-0.017	0.0602	0.194	0.024	0.2096	91.1292	3.8011	154.3182
9	0.638	0.3349	0.0323	2.2069	-1.1209	1.8959	-0.1533	0.2842	0.0147	-0.6429	0.3146	0.2501	0.4205	-0.3774	-0.1481	0.2717	0.0444	-0.0245	0.298	-0.0298	0.2333	47.1113	2.94	178.2507
10	2.5255	3.069	-1.4814	5.0096	-1.3377	1.7567	0.0625	-0.3649	0.1891	-0.8219	-0.2692	-0.0344	0.1161	0.1948	0.1659	0.3553	0.0192	0.0176	0.4289	0.0709	0.2541	57.8408	16.8809	176.2474
11	0.6044	0.7109	-0.0558	0.7443	-0.4626	0.2096	-0.0607	0.2163	0.0364	-0.0267	0.0937	0.0142	-0.188	0.1119	-0.0145	0.2643	-0.0226	0.0544	0.2401	-0.0093	0.2157	63.2749	23.229	188.7745
12	2.3526	-0.1311	0.8055	2.0669	-0.0844	3.0873	0.0295	0.3382	0.4928	0.2922	-0.0929	0.5343	-0.2977	-0.5018	0.1644	0.2578	-0.0188	0.0753	0.2867	0.0278	0.2555	56.2279	30.4425	185.6845
13	2.1012	1.5604	0.3289	3.3641	-0.2533	2.0495	0.2478	-0.1541	0.4943	-0.3261	-0.2202	1.4434	-0.3205	-0.7127	-0.1014	0.3512	0.0281	-0.0863	0.5664	-0.0139	0.6062	41.491	16.4387	175.4438
14	0.4521	0.5292	-0.1386	1.9074	-1.0129	0.7158	0.0595	0.0914	-0.0252	-0.4627	0.0161	-0.0677	-0.2593	0.1135	0.0166	0.2507	-0.0246	0.0286	0.1693	0.0184	0.2325	59.637	13.4816	191.4737
15	1.7353	0.6288	-0.0447	2.2354	0.1701	2.3609	0.0404	0.0597	-0.092	0.1533	0.0189	-0.0839	0.0488	-0.048	-0.043	0.1404	0.0429	0.034	0.1047	0.0178	0.1547	52.6502	-1.4969	199.9256
16	3.1494	-0.3153	0.8487	3.8356	-0.2888	3.6294	-0.4355	-0.1459	0.5448	-0.2634	-0.5617	1.2196	0.1351	-0.8745	0.3583	0.3122	-0.0588	-0.018	0.3305	-0.0355	0.5182	37.0194	-9.0198	198.4341
17	-0.1046	-0.0942	-0.2283	1.308	-0.0891	0.5371	0.0142	0.0043	-0.0516	-0.0929	0.0651	-0.003	0.2388	-0.0636	-0.0655	0.212	0.0011	-0.0206	0.1533	-0.0149	0.1515	113.005	14.155	104.8213
18	0.2942	-0.1947	-0.2384	0.4759	0.2899	1.4332	-0.045	0.0385	0.0411	-0.4203	0.0438	-0.091	-0.59	0.1624	-0.0098	0.3844	-0.0591	-0.045	0.1447	0.0083	0.1419	118.8186	35.5131	111.23
19	1.4761	1.6599	0.4808	2.3885	0.0771	4.7022	-0.0422	0.1666	-0.4313	-0.1585	0.2147	-0.7714	0.1248	1.0485	-0.0401	0.1382	-0.0492	-0.0168	0.2248	0.0093	0.2401	128.0471	32.6566	115.8201
20	3.3962	0.5113	0.8716	3.7841	-0.0345	3.5785	0.2915	-0.1379	-0.6099	0.1195	-0.0405	-0.5696	0.3518	0.5889	-0.1861	0.3229	0.0505	-0.0471	0.2939	-0.0217	0.4146	124.0075	9.3931	109.5102
21	2.0332	-1.2445	0.4897	3.2742	-0.6901	1.9796	-0.0397	0.2554	0.1053	-0.5033	-0.0477	-0.4011	-0.1771	0.237	0.0622	0.3282	-0.0186	0.0004	0.1673	0.0153	0.1945	121.6704	33.7367	105.3885
22	2.1883	1.5705	1.1185	3.558	0.9356	4.0363	0.5689	0.1866	-0.3201	0.5994	-0.3555	0.7071	-0.1136	-0.2608	-0.1113	0.4682	0.0407	0.004	0.3626	-0.14	0.5579	102.8877	25.6576	94.3932
23	0.4982	1.4848	0.0639	4.5509	0.648	2.9456	0.0296	0.0545	0.0974	-0.786	-0.2194	0.1486	-0.2722	0.1556	0.1601	0.4875	0.0207	-0.0313	0.2016	-0.0081	0.1923	114.3651	27.2146	84.2172
24	1.696	0.0078	0.3517	1.0712	1.0689	3.3909	-0.5992	0.2815	-0.0306	-0.0544	0.0283	-0.1574	0.2416	-0.1025	-1.4087	1.4363	0.004	0.1019	0.2735	-0.1798	0.0747	116.6088	15.7161	74.557
25	0.5074	0.459	0.2608	0.9576	-0.9261	3.6583	-0.0333	-0.0399	-0.0346	-0.1811	0.0844	0.0531	1.0037	-0.4112	-0.0399	0.3728	-0.0604	-0.0484	0.3085	-0.0117	0.2706	61.1958	6.1171	148.0872
26	0.6703	0.6629	-0.7684	2.0539	0.5947	2.3965	0.0376	-0.1972	-0.0067	0.157	0.0114	-0.0489	0.358	-0.0446	-0.0915	0.2811	0.0587	-0.0223	0.3744	0.0199	0.1938	65.5963	15.4405	160.9988
27	0.8677	0.9357	0.1324	0.5771	0.0013	4.8472	0.1585	0.0465	0.0838	-0.0458	0.0601	-0.0241	-0.8241	0.4217	-0.2241	0.3658	-0.0372	0.0461	0.3156	0.0257	0.2403	76.2888	33.5205	166.3828
28	3.6667	0.1436	1.6791	3.0918	1.049	5.0993	0.1184	0.2095	-0.5256	0.2425	0.3701	-0.4499	0.2648	0.1051	-0.036	0.4917	0.0094	-0.2077	0.3613	0.0395	0.3326	72.992	2.6288	165.9474
29	1.0069	-0.2432	-1.151	3.9434	-0.1251	2.0897	0.0114	0.3662	-0.4223	-1.1006	0.0737	-0.703	0.1479	0.4381	-0.0318	0.3369	0.0643	-0.0255	0.5009	-0.0833	0.4338	74.177	6.8873	156.2322
30	1.7682	-0.3366	1.1555	2.3442	0.1818	2.5698	-0.0635	0.1909	-0.0885	-0.0688	0.0347	-0.0634	-0.0929	-0.0699	0.0568	0.3552	0.0118	0.076	0.3512	-0.0218	0.2654	70.0961	27.3272	154.1347
31	1.0418	0.6334	0.1037	2.3773	-0.3881	2.3648	0.0573	-0.1765	0.1403	-0.0532	-0.0826	0.2667	-0.1253	-0.2945	0.037	0.2388	-0.0243	0.018	0.3332	-0.0502	0.2247	62.2124	19.0204	138.6407
32	1.9222	0.599	0.1152	2.0235	0.4473	2.3849	-0.0597	0.0102	0.0504	-0.3119	0.0313	0.0324	-0.072	-0.0483	0.0141	0.3427	0.0089	0.0251	0.3084	0.0313	0.2081	67.1486	23.6754	132.3944

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 134:169)
2	X-RAY DIFFRACTION	2	(chain A and resid 170:233)
3	X-RAY DIFFRACTION	3	(chain A and resid 234:243)
4	X-RAY DIFFRACTION	4	(chain A and resid 244:288)
5	X-RAY DIFFRACTION	5	(chain A and resid 289:313)
6	X-RAY DIFFRACTION	6	(chain A and resid 314:351)
7	X-RAY DIFFRACTION	7	(chain A and resid 352:436)
8	X-RAY DIFFRACTION	8	(chain A and resid 437:463)
9	X-RAY DIFFRACTION	9	(chain B and resid 134:176)
10	X-RAY DIFFRACTION	10	(chain B and resid 177:191)
11	X-RAY DIFFRACTION	11	(chain B and resid 192:249)
12	X-RAY DIFFRACTION	12	(chain B and resid 250:271)
13	X-RAY DIFFRACTION	13	(chain B and resid 272:313)
14	X-RAY DIFFRACTION	14	(chain B and resid 314:354)
15	X-RAY DIFFRACTION	15	(chain B and resid 355:455)
16	X-RAY DIFFRACTION	16	(chain B and resid 456:463)
17	X-RAY DIFFRACTION	17	(chain C and resid 134:190)
18	X-RAY DIFFRACTION	18	(chain C and resid 191:248)
19	X-RAY DIFFRACTION	19	(chain C and resid 249:269)
20	X-RAY DIFFRACTION	20	(chain C and resid 270:311)
21	X-RAY DIFFRACTION	21	(chain C and resid 312:340)
22	X-RAY DIFFRACTION	22	(chain C and resid 341:359)
23	X-RAY DIFFRACTION	23	(chain C and resid 360:452)
24	X-RAY DIFFRACTION	24	(chain C and resid 453:463)
25	X-RAY DIFFRACTION	25	(chain D and resid 134:172)
26	X-RAY DIFFRACTION	26	(chain D and resid 173:210)
27	X-RAY DIFFRACTION	27	(chain D and resid 211:268)
28	X-RAY DIFFRACTION	28	(chain D and resid 269:288)
29	X-RAY DIFFRACTION	29	(chain D and resid 289:314)
30	X-RAY DIFFRACTION	30	(chain D and resid 315:350)
31	X-RAY DIFFRACTION	31	(chain D and resid 351:393)
32	X-RAY DIFFRACTION	32	(chain D and resid 394:463)

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