PDB-6cni: Crystal structure of H105A PGAM5 dimer

ID or keywords:

Entry

Database: PDB / ID: 6cni

Title

Crystal structure of H105A PGAM5 dimer

Components

Serine/threonine-protein phosphatase PGAM5, mitochondrial

Keywords

SIGNALING PROTEIN / Phosphatase / Mitophagy

Function / homology

Function and homology information

negative regulation of cold-induced thermogenesis / myosin phosphatase activity / positive regulation of mitochondrial fission / Receptor Mediated Mitophagy / protein serine/threonine phosphatase activity / protein-serine/threonine phosphatase / phosphatase activity / necroptotic process / GTPase activator activity / macroautophagy ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.7 Å

Authors

Ruiz, K. / Agnew, C. / Jura, N.

Citation

Journal: Nat Commun / Year: 2019
Title: Functional role of PGAM5 multimeric assemblies and their polymerization into filaments.
Authors: Ruiz, K. / Thaker, T.M. / Agnew, C. / Miller-Vedam, L. / Trenker, R. / Herrera, C. / Ingaramo, M. / Toso, D. / Frost, A. / Jura, N.

History

Deposition	Mar 8, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 13, 2019	Provider: repository / Type: Initial release
Revision 1.1	Oct 4, 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 / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6cni.cif.gz	170 KB	Display	PDBx/mmCIF format
PDB format	pdb6cni.ent.gz	131.9 KB	Display	PDB format
PDBx/mmJSON format	6cni.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6cni_validation.pdf.gz	448.5 KB	Display	wwPDB validaton report
Full document	6cni_full_validation.pdf.gz	448.8 KB	Display
Data in XML	6cni_validation.xml.gz	18.3 KB	Display
Data in CIF	6cni_validation.cif.gz	26.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cn/6cni ftp://data.pdbj.org/pub/pdb/validation_reports/cn/6cni	HTTPS FTP

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Related structure data

Related structure data	6cnlC 3mxoS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4ae9-1 5n3r-d 3mxo-d 3gq3-d 1xha-1 1ctp-d 3gpu-d 4c34-d 6s9b-d 1cmk-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	#257 - May 2021 Fetal Hemoglobin similarity (4) #50 - Feb 2004 Glycolytic Enzymes similarity (4) #225 - Sep 2018 Phytase similarity (1) #141 - Sep 2011 O-GlcNAc Transferase similarity (1) #43 - Jul 2003 Src Tyrosine Kinase similarity (1) #60 - Dec 2004 Ubiquitin similarity (1)

Deposited unit

A: Serine/threonine-protein phosphatase PGAM5, mitochondrial

B: Serine/threonine-protein phosphatase PGAM5, mitochondrial

hetero molecules

51.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	71.003, 72.018, 81.941
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Serine/threonine-protein phosphatase PGAM5, mitochondrial / Bcl-XL-binding protein v68 / Phosphoglycerate mutase family member 5 Mass: 25407.885 Da / Num. of mol.: 2 / Mutation: H105A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PGAM5 / Production host: Escherichia coli (E. coli) References: UniProt: Q96HS1, protein-serine/threonine phosphatase
#2: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#3: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 308 / 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: 2.06 Å³/Da / Density % sol: 40.33 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M HEPES, pH 7.5 0.2 M MgCl2 30% PEG 400

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.12 Å
Detector	Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 23, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.12 Å / Relative weight: 1
Reflection	Resolution: 1.7→43.029 Å / Num. obs: 89093 / % possible obs: 99.73 % / Redundancy: 12.1 % / B_iso Wilson estimate: 20.46 Å² / CC_1/2: 1 / R_merge(I) obs: 0.07524 / R_pim(I) all: 0.02242 / R_rim(I) all: 0.07861 / Net I/σ(I): 21.78
Reflection shell	Resolution: 1.7→1.761 Å / Redundancy: 7.8 % / R_merge(I) obs: 0.7598 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 4520 / CC_1/2: 0.807 / R_pim(I) all: 0.2861 / R_rim(I) all: 0.8144 / % possible all: 97.54

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Processing

Software

Name	Version	Classification
PHENIX	(1.13_2998: ???)	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3MXO

3mxo

Resolution: 1.7→43.029 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 0.42 / Phase error: 20.12

	R_factor	Num. reflection	% reflection
R_free	0.197	2230	4.74 %
R_work	0.1711	-	-
obs	0.1724	89093	99.74 %

Solvent computation

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

Displacement parameters

B_iso mean: 27.24 Å²

Refinement step

Cycle: LAST / Resolution: 1.7→43.029 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2874	0	16	308	3198

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	2962
X-RAY DIFFRACTION	f_angle_d	0.794	4029
X-RAY DIFFRACTION	f_dihedral_angle_d	11.165	2415
X-RAY DIFFRACTION	f_chiral_restr	0.056	465
X-RAY DIFFRACTION	f_plane_restr	0.006	519

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 (%)
1.7-1.7193	0.33	133	0.2633	2767	X-RAY DIFFRACTION	96
1.7193-1.7396	0.3381	124	0.259	2760	X-RAY DIFFRACTION	98
1.7396-1.7608	0.2758	131	0.2538	2827	X-RAY DIFFRACTION	99
1.7608-1.7831	0.2708	185	0.2316	2808	X-RAY DIFFRACTION	100
1.7831-1.8065	0.2539	178	0.2098	2803	X-RAY DIFFRACTION	100
1.8065-1.8313	0.2098	135	0.2069	2821	X-RAY DIFFRACTION	100
1.8313-1.8574	0.2139	149	0.19	2812	X-RAY DIFFRACTION	100
1.8574-1.8852	0.2289	123	0.1962	2872	X-RAY DIFFRACTION	100
1.8852-1.9146	0.2252	108	0.1847	2881	X-RAY DIFFRACTION	100
1.9146-1.946	0.2356	125	0.1868	2901	X-RAY DIFFRACTION	100
1.946-1.9796	0.209	146	0.1748	2770	X-RAY DIFFRACTION	100
1.9796-2.0156	0.1938	106	0.1715	2833	X-RAY DIFFRACTION	100
2.0156-2.0543	0.2022	125	0.1715	2880	X-RAY DIFFRACTION	100
2.0543-2.0963	0.2204	155	0.176	2847	X-RAY DIFFRACTION	100
2.0963-2.1418	0.1988	149	0.1628	2795	X-RAY DIFFRACTION	100
2.1418-2.1917	0.2266	167	0.1628	2789	X-RAY DIFFRACTION	100
2.1917-2.2465	0.2153	162	0.1706	2849	X-RAY DIFFRACTION	100
2.2465-2.3072	0.1928	168	0.1529	2795	X-RAY DIFFRACTION	100
2.3072-2.3751	0.1853	165	0.1656	2816	X-RAY DIFFRACTION	100
2.3751-2.4517	0.1996	133	0.1675	2834	X-RAY DIFFRACTION	100
2.4517-2.5394	0.2086	132	0.1758	2852	X-RAY DIFFRACTION	100
2.5394-2.641	0.2388	117	0.1725	2860	X-RAY DIFFRACTION	100
2.641-2.7612	0.1819	115	0.171	2850	X-RAY DIFFRACTION	100
2.7612-2.9067	0.2232	123	0.1753	2868	X-RAY DIFFRACTION	100
2.9067-3.0888	0.1699	118	0.1861	2866	X-RAY DIFFRACTION	100
3.0888-3.3272	0.19	137	0.1748	2837	X-RAY DIFFRACTION	100
3.3272-3.6619	0.1694	170	0.1643	2784	X-RAY DIFFRACTION	100
3.6619-4.1914	0.15	183	0.1463	2822	X-RAY DIFFRACTION	100
4.1914-5.2792	0.1521	93	0.1313	2856	X-RAY DIFFRACTION	100
5.2792-43.0431	0.2154	171	0.1851	2812	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	1.7332	0.4276	1.9362	0.846	0.8159	5.9071	-0.0245	-0.1268	0.1398	-0.0025	-0.0861	0.1361	-0.1096	-0.5404	0.1375	0.112	0.0067	0.0135	0.1272	0.0212	0.1359	12.0108	2.1806	-22.6254
2	3.6106	-2.2114	-2.3513	6.8464	5.412	9.0137	0.0953	-0.0867	0.4028	0.0292	0.1075	-0.2681	-0.3497	0.198	-0.2419	0.1222	-0.038	-0.003	0.0932	0.017	0.1392	24.7756	6.6273	-14.1464
3	6.3301	-0.4413	-0.3774	1.068	0.4348	1.4288	-0.0451	0.0994	0.3881	-0.021	0.0258	0.053	-0.2486	-0.0686	-0.0003	0.2033	0.0127	-0.0226	0.093	0.0325	0.1564	11.3023	8.9947	-20.3683
4	5.9169	-1.4829	-7.2332	9.2851	-2.8881	2.0351	0.6154	0.1058	0.5857	0.0978	-0.0258	0.0011	-0.7042	0.015	-0.5638	0.2517	-0.0069	-0.0217	0.2812	0.003	0.1585	9.8084	3.1702	-37.9359
5	2.8983	0.386	0.3918	2.6353	0.5182	3.2412	0.0018	-0.0361	-0.1389	0.0944	0.0559	0.3103	0.0909	-0.1982	-0.0583	0.1277	0.0192	-0.0054	0.1143	0.0133	0.1757	9.5112	-2.8673	-19.8449
6	9.5465	-5.8767	9.1736	6.1391	-7.5161	2.0196	0.2936	0.2512	-0.36	-0.237	0.004	-0.0585	0.5083	0.1601	-0.3106	0.139	-0.004	-0.0053	0.1648	-0.0177	0.1188	11.2801	-8.8005	-30.2655
7	5.0554	-0.3972	3.5064	7.0746	4.5812	9.9079	-0.0646	0.0544	0.0458	0.1668	0.1204	-0.1702	0.032	0.4432	-0.0603	0.1259	-0.0012	0.0083	0.1177	0.0269	0.1213	24.1041	-3.535	-11.073
8	2.7756	0.5762	2.8736	2.1758	1.7635	3.5774	0.1695	-0.7751	-0.1394	0.44	-0.0189	0.4066	0.4041	-0.2996	-0.0715	0.29	0.0064	0.0524	0.1954	0.0638	0.2702	12.4673	-20.5496	-7.0931
9	5.6738	-0.2205	0.2778	6.5077	4.7572	7.5056	0.0011	0.7187	-0.8505	-0.4756	0.1325	-0.0708	0.7226	0.0968	-0.185	0.3189	0.0128	-0.0014	0.29	-0.1214	0.2778	27.7655	-29.509	-30.6892
10	2.318	0.622	0.4615	4.122	0.2424	2.6507	0.0185	0.054	-0.233	0.1545	0.0405	-0.165	0.1063	0.1898	-0.046	0.1002	0.0512	-0.019	0.1283	-0.0061	0.1542	28.8979	-20.9367	-15.2676
11	5.0524	1.7683	2.5242	2.7167	1.5278	3.7108	0.1664	0.1009	-0.6415	0.1707	0.0612	-0.1722	0.5149	0.1661	-0.2475	0.2148	0.0485	-0.0107	0.1369	-0.0201	0.2444	26.3507	-29.0689	-16.1467
12	6.1844	3.9386	8.0904	6.3948	7.8789	2.0459	0.141	0.2083	-0.3311	-0.0131	0.1182	-0.3706	0.2426	0.1791	-0.2105	0.2353	-0.041	0.0622	0.2201	0.038	0.3138	7.6666	-32.2918	-20.2567
13	3.8984	-0.9542	2.292	2.8091	1.3979	2.913	0.1123	-0.3451	-0.2576	0.2374	0.0557	0.2848	0.1889	-0.2489	-0.1359	0.1621	-0.0272	0.0299	0.1342	0.0495	0.1837	14.1147	-22.5558	-13.055
14	4.0097	-0.6897	-1.4144	2.2899	-0.357	4.7196	0.0686	-0.0511	0.0237	0.0437	0.0617	0.4291	-0.0833	-0.2918	-0.1154	0.1414	-0.0058	0.0151	0.0838	0.0041	0.2072	11.2014	-15.7278	-16.1764
15	9.038	-1.0598	-2.5746	7.7505	3.3933	8.7646	0.1627	0.3155	-0.0486	-0.3082	-0.0677	-0.1658	-0.1669	0.3167	-0.0965	0.1431	-0.0154	-0.0133	0.143	0.0161	0.114	26.5752	-12.4518	-24.9078

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 88 through 114 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 115 through 138 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 139 through 211 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 212 through 222 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 223 through 264 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 265 through 274 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 275 through 289 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 89 through 104 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 105 through 121 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 122 through 150 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 151 through 193 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 194 through 211 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 212 through 241 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 242 through 274 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 275 through 289 )

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