PDB-4oag: Crystal structure of the cytosolic domain of mouse MiD51 bound to ADP

ID or keywords:

Entry

Database: PDB / ID: 4oag

Title

Crystal structure of the cytosolic domain of mouse MiD51 bound to ADP

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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PDBx/mmCIF format	4oag.cif.gz	279.7 KB	Display	PDBx/mmCIF format
PDB format	pdb4oag.ent.gz	226.5 KB	Display	PDB format
PDBx/mmJSON format	4oag.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/4oag ftp://data.pdbj.org/pub/pdb/validation_reports/oa/4oag	HTTPS FTP

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Related structure data

Related structure data	4oafC 4oahC 4oaiC C: citing same article (ref.)
Similar structure data	4nxu-5 6aj3-d 4oaf-2 4nxv-6 3h7n-4 3h7n-3 3cdg-1 4oah-2 3h7n-1 3cdg-2 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

hetero molecules

75.5 kDa, 2 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)	62.068, 80.811, 65.376
Angle α, β, γ (deg.)	90.00, 105.74, 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: 37252.750 Da / Num. of mol.: 2 / Fragment: Cytosolic domain, unp residues 134-463 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-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₅O₁₀P₂ / Comment: ADP, energy-carrying molecule*YM
#3: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 531 / 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: 2.12 Å³/Da / Density % sol: 42.06 %
Crystal grow	Temperature: 296.15 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 100 mM Bis-Tris, 100 mM lithium sulfate, 10 mM magnesiun chloride, 25% PEG 3350, 10 mM ADP, pH 7.0, 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: 1.01 Å

Detector

Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 1, 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: 1.01 Å / Relative weight: 1

Reflection

Resolution: 1.939→34.705 Å / Num. all: 44016 / Num. obs: 44016 / % possible obs: 95.6 % / Redundancy: 3.4 % / R_sym value: 0.059 / Net I/σ(I): 15.6

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	R_sym value	Diffraction-ID	% possible all
1.94-2.04	2.9	0.442	1.8	0.442	1	82.2
2.04-2.17	3.5	0.314	2.5	0.314	1	98.4
2.17-2.32	3.4	0.214	3.6	0.214	1	97.4
2.32-2.5	3.5	0.154	5	0.154	1	97.9
2.5-2.74	3.5	0.108	7.2	0.108	1	98.1
2.74-3.07	3.4	0.068	11.3	0.068	1	97.5
3.07-3.54	3.5	0.041	18.5	0.041	1	98.3
3.54-4.34	3.5	0.026	27.6	0.026	1	97.4
4.34-6.13	3.4	0.022	30	0.022	1	97.7
6.13-34.705	3.4	0.018	33.2	0.018	1	97.5

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

	Highest resolution	Lowest resolution
Rotation	5.3 Å	34.7 Å
Translation	5.3 Å	34.7 Å

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Processing

Software

Name	Version	Classification
SCALA	3.3.20	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→33.999 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.2 / σ(F): 1.34 / Phase error: 22.62 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2162	2003	4.88 %
R_work	0.1709	-	-
obs	0.1731	41027	97.55 %

Solvent computation

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

Displacement parameters

B_iso mean: 30.8489 Å²

Refinement step

Cycle: LAST / Resolution: 2→33.999 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5098	0	59	531	5688

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	5268
X-RAY DIFFRACTION	f_angle_d	1.148	7195
X-RAY DIFFRACTION	f_dihedral_angle_d	15.211	1943
X-RAY DIFFRACTION	f_chiral_restr	0.072	835
X-RAY DIFFRACTION	f_plane_restr	0.005	914

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 (%)
2-2.05	0.2976	135	0.2282	2724	X-RAY DIFFRACTION	96
2.05-2.1054	0.325	149	0.2007	2794	X-RAY DIFFRACTION	98
2.1054-2.1674	0.2269	153	0.192	2788	X-RAY DIFFRACTION	98
2.1674-2.2373	0.2396	137	0.1835	2788	X-RAY DIFFRACTION	98
2.2373-2.3173	0.2314	143	0.1853	2740	X-RAY DIFFRACTION	96
2.3173-2.41	0.2453	126	0.1866	2769	X-RAY DIFFRACTION	97
2.41-2.5197	0.2428	160	0.1905	2812	X-RAY DIFFRACTION	99
2.5197-2.6525	0.2462	138	0.1855	2800	X-RAY DIFFRACTION	98
2.6525-2.8186	0.2547	139	0.1873	2781	X-RAY DIFFRACTION	97
2.8186-3.0361	0.2383	143	0.1764	2757	X-RAY DIFFRACTION	97
3.0361-3.3414	0.1903	147	0.1593	2820	X-RAY DIFFRACTION	98
3.3414-3.8243	0.1731	140	0.1512	2753	X-RAY DIFFRACTION	96
3.8243-4.8161	0.1838	147	0.1374	2861	X-RAY DIFFRACTION	99
4.8161-34.0042	0.1994	146	0.1758	2837	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	0.8413	0.1313	-0.1507	1.6103	-0.49	0.739	0.0131	0.0982	0.1697	-0.1426	0.1171	0.3094	0.0475	-0.1717	-0.1775	0.2257	0.0137	0.0248	0.2427	0.0093	0.2535	67.8855	-12.4073	10.7709
2	1.2295	-0.3312	0.0585	1.7521	-0.5985	0.3698	0.0102	-0.0039	-0.0347	-0.1174	0.0314	-0.0635	0.0147	0.0473	-0.034	0.234	-0.0228	0.0247	0.1922	-0.0433	0.1816	81.985	-22.6375	13.1542
3	7.7818	4.2766	-3.9649	2.8154	-2.242	6.0537	-0.3132	-0.6172	-1.0654	0.0696	-0.2482	-0.6611	0.3201	0.7403	0.4691	0.2903	0.0421	0.1204	0.2837	0.1051	0.4468	87.5997	-43.0818	24.4183
4	1.5705	-0.7852	0.988	2.7154	-0.8567	2.0407	0.1179	0.153	-0.2134	-0.5288	-0.0659	0.4508	0.2476	-0.1793	0.0044	0.265	-0.0409	-0.0029	0.2304	-0.0305	0.2551	69.3128	-31.9303	10.4939
5	3.6195	-1.3731	0.8466	3.1518	-0.788	1.9317	-0.14	0.8087	0.3265	-0.5203	-0.1478	0.0904	-0.0384	0.0792	0.1587	0.2986	-0.055	-0.0138	0.2978	-0.021	0.2501	69.0984	-19.8177	6.4039
6	1.3265	-0.2624	-0.3675	1.1126	-0.9359	1.111	0.0688	0.0781	0.0399	0.0589	-0.0487	0.0419	-0.111	-0.0028	-0.0226	0.2707	-0.0276	0.0457	0.2439	0.0029	0.2152	83.9222	-12.6267	9.0851
7	0.8702	-0.5385	-0.3024	2.3456	0.3345	1.9281	0.0453	0.0102	0.0676	0.1801	-0.043	-0.0982	-0.049	0.0128	-0.0102	0.2908	-0.0212	0.0775	0.2183	0.0081	0.2553	91.3014	-6.0178	3.2184
8	4.8957	-2.2243	0.34	7.8816	-1.3038	4.0254	0.0822	0.7231	-0.0536	-1.1481	-0.0732	0.3936	0.1399	-0.4309	-0.0307	0.4033	-0.0362	0.0379	0.3047	0.0081	0.2661	86.2629	-1.28	-10.7648
9	6.1008	2.2037	-0.7815	5.6562	-0.6809	4.6555	0.1133	-0.233	0.2174	0.012	-0.1936	0.0669	0.0556	0.1795	0.1242	0.215	0.0306	0.0631	0.146	0.0181	0.2438	34.3768	-13.2487	40.6593
10	2.0186	-0.849	-0.8085	1.3236	0.8077	0.8548	0.0601	0.0228	0.0672	-0.0062	-0.0116	-0.0859	-0.0385	-0.0094	-0.0704	0.1923	-0.0083	0.0233	0.1618	0.0029	0.175	64.2951	-29.8284	33.532
11	2.3839	-0.5936	-0.0994	4.2145	0.3885	2.1172	-0.121	-0.0438	0.0434	0.3808	0.3218	-0.3087	-0.0674	0.0769	-0.2227	0.2554	0.0506	-0.0369	0.2332	-0.0235	0.2471	74.8233	-34.3201	39.1479
12	1.8262	-0.1698	0.3116	1.4846	1.1737	2.2661	-0.0934	-0.2385	0.4104	0.2029	0.0066	0.2285	-0.1317	0.1407	0.0248	0.24	-0.0148	0.0602	0.1942	-0.032	0.3012	62.701	-23.6039	40.1187
13	5.8407	-3.8437	5.8644	4.3176	-2.4489	7.0408	-0.235	0.2673	0.3271	-0.2356	0.104	-0.0675	-0.3459	-0.0554	0.1366	0.2995	-0.0134	0.0711	0.2703	0.016	0.2615	43.6201	-28.3708	27.8656
14	1.3141	-0.183	-0.5717	2.0135	0.2744	0.8442	-0.0102	0.0917	-0.048	0.2331	-0.0995	-0.0106	0.2139	-0.0053	0.0785	0.1997	-0.0055	0.0081	0.1926	0.0099	0.2169	40.9273	-25.4298	40.641
15	2.6184	0.2522	1.4252	3.3249	-0.5138	6.0023	0.1827	0.2408	-0.1171	-0.1336	-0.0525	0.4585	0.2306	-0.2912	-0.0899	0.1456	0.0041	0.0008	0.1887	-0.0221	0.2123	30.1059	-27.272	35.659
16	2.9264	-0.9237	0.499	2.9487	-0.3687	1.3371	-0.0118	-0.3623	0.0677	0.447	0.0846	0.0815	0.0238	-0.1025	-0.0287	0.296	-0.0556	0.1017	0.2445	-0.019	0.2687	39.3836	-31.9669	48.9028

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 134:185 )	A	134 - 185
2	X-RAY DIFFRACTION	2	( CHAIN A AND RESID 186:233 )	A	186 - 233
3	X-RAY DIFFRACTION	3	( CHAIN A AND RESID 234:243 )	A	234 - 243
4	X-RAY DIFFRACTION	4	( CHAIN A AND RESID 244:291 )	A	244 - 291
5	X-RAY DIFFRACTION	5	( CHAIN A AND RESID 294:320 )	A	294 - 320
6	X-RAY DIFFRACTION	6	( CHAIN A AND RESID 321:373 )	A	321 - 373
7	X-RAY DIFFRACTION	7	( CHAIN A AND RESID 374:444 )	A	374 - 444
8	X-RAY DIFFRACTION	8	( CHAIN A AND RESID 445:463 )	A	445 - 463
9	X-RAY DIFFRACTION	9	( CHAIN B AND RESID 134:148 )	B	134 - 148
10	X-RAY DIFFRACTION	10	( CHAIN B AND RESID 149:243 )	B	149 - 243
11	X-RAY DIFFRACTION	11	( CHAIN B AND RESID 244:273 )	B	244 - 273
12	X-RAY DIFFRACTION	12	( CHAIN B AND RESID 276:342 )	B	276 - 342
13	X-RAY DIFFRACTION	13	( CHAIN B AND RESID 343:355 )	B	343 - 355
14	X-RAY DIFFRACTION	14	( CHAIN B AND RESID 356:392 )	B	356 - 392
15	X-RAY DIFFRACTION	15	( CHAIN B AND RESID 393:413 )	B	393 - 413
16	X-RAY DIFFRACTION	16	( CHAIN B AND RESID 414:463 )	B	414 - 463

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