PDB-5f9c: Crystal structure of the G121R mutant of human phosphoglucomutase 1

ID or keywords:

Entry

Database: PDB / ID: 5f9c

Title

Crystal structure of the G121R mutant of human phosphoglucomutase 1

Components

Phosphoglucomutase-1

PGM1

Keywords

ISOMERASE / isomerase metabolism

Function / homology

Function and homology information

Defective PGM1 causes PGM1-CDG / Galactose catabolism / phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) /

phosphoglucomutase activity / Glycogen breakdown (glycogenolysis) /

Glycogen synthesis /

gluconeogenesis / glycolytic process / glucose metabolic process / tertiary granule lumen ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 2.5 Å

Authors

Beamer, L.J.

Citation

Journal: J.Mol.Biol. / Year: 2016
Title: Induced Structural Disorder as a Molecular Mechanism for Enzyme Dysfunction in Phosphoglucomutase 1 Deficiency.
Authors: Stiers, K.M. / Kain, B.N. / Graham, A.C. / Beamer, L.J.

History

Deposition	Dec 9, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 27, 2016	Provider: repository / Type: Initial release
Revision 1.1	Nov 22, 2017	Group: Database references / Derived calculations / Refinement description Category: citation / pdbx_struct_oper_list / software Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2	Sep 27, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5f9c.cif.gz	426.1 KB	Display	PDBx/mmCIF format
PDB format	pdb5f9c.ent.gz	351.5 KB	Display	PDB format
PDBx/mmJSON format	5f9c.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/f9/5f9c ftp://data.pdbj.org/pub/pdb/validation_reports/f9/5f9c	HTTPS FTP

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Related structure data

Related structure data	5epcSC 5hshC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4oes-d 2xja-3 3pmg-1 4dcx-1 1uiu-2 1jdy-2 4dcy-1 4ow6-1 4qfk-2 4qfk-7 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	#44 - Aug 2003 Calmodulin similarity (1) #60 - Dec 2004 Ubiquitin similarity (1) #196 - Apr 2016 Lead Poisoning similarity (1) #28 - Apr 2002 Anthrax Toxin similarity (1) #234 - Jun 2019 MDM2 and Cancer similarity (1)

Deposited unit

A: Phosphoglucomutase-1

B: Phosphoglucomutase-1

hetero molecules

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

1

A: Phosphoglucomutase-1

hetero molecules

defined by author
62.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Phosphoglucomutase-1

hetero molecules

defined by author
62.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	171.980, 171.980, 99.900
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	92
Space group name H-M	P4₁2₁2

#1: Protein	Phosphoglucomutase-1 / PGM1 / PGM 1 / Glucose phosphomutase 1 Mass: 61619.027 Da / Num. of mol.: 2 / Mutation: G121R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PGM1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P36871, phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent)
#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.97 Å³/Da / Density % sol: 58.65 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 1.5 M ammonium sulfate with 0.15 lithium sulfate and 0.1 CAPS buffer, pH 10.5 PH range: 10.5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.00001 Å
Detector	Type: RDI CMOS_8M / Detector: CMOS / Date: Oct 25, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.00001 Å / Relative weight: 1
Reflection	Resolution: 2.35→60.943 Å / Num. obs: 71761 / % possible obs: 99.8 % / Redundancy: 14.1 % / B_iso Wilson estimate: 55.3 Å² / R_merge(I) obs: 0.123 / Net I/σ(I): 16.5
Reflection shell	Resolution: 2.35→2.41 Å / Redundancy: 12.4 % / R_merge(I) obs: 3.101 / Mean I/σ(I) obs: 0.8 / % possible all: 99.2

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
XDS		data reduction
XDS		data scaling

Refinement

Starting model: 5EPC

5epc

Resolution: 2.5→60.943 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 28.33 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2427	4983	5.04 %
R_work	0.1918	-	-
obs	0.1944	71761	99.8 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.5→60.943 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8051	0	59	80	8190

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	8249
X-RAY DIFFRACTION	f_angle_d	1.125	11205
X-RAY DIFFRACTION	f_dihedral_angle_d	13.288	2879
X-RAY DIFFRACTION	f_chiral_restr	0.046	1294
X-RAY DIFFRACTION	f_plane_restr	0.006	1451

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 (%)
2.5-2.5284	0.3283	141	0.3367	3127	X-RAY DIFFRACTION	99
2.5284-2.5582	0.3445	151	0.3181	3134	X-RAY DIFFRACTION	99
2.5582-2.5894	0.3918	162	0.3245	3073	X-RAY DIFFRACTION	99
2.5894-2.6221	0.3161	181	0.3225	3118	X-RAY DIFFRACTION	100
2.6221-2.6567	0.3615	196	0.3161	3095	X-RAY DIFFRACTION	100
2.6567-2.693	0.3598	173	0.3095	3128	X-RAY DIFFRACTION	100
2.693-2.7315	0.3412	195	0.2965	3081	X-RAY DIFFRACTION	100
2.7315-2.7723	0.3708	154	0.2877	3170	X-RAY DIFFRACTION	100
2.7723-2.8156	0.3311	139	0.2735	3115	X-RAY DIFFRACTION	100
2.8156-2.8618	0.3626	172	0.2705	3140	X-RAY DIFFRACTION	100
2.8618-2.9111	0.3442	154	0.2696	3116	X-RAY DIFFRACTION	100
2.9111-2.9641	0.269	175	0.2616	3148	X-RAY DIFFRACTION	100
2.9641-3.0211	0.3124	182	0.2412	3120	X-RAY DIFFRACTION	100
3.0211-3.0827	0.3069	165	0.2431	3108	X-RAY DIFFRACTION	100
3.0827-3.1498	0.3306	148	0.2347	3146	X-RAY DIFFRACTION	100
3.1498-3.223	0.3176	157	0.2223	3160	X-RAY DIFFRACTION	100
3.223-3.3036	0.2356	184	0.2021	3112	X-RAY DIFFRACTION	100
3.3036-3.3929	0.2742	148	0.2177	3142	X-RAY DIFFRACTION	100
3.3929-3.4928	0.2303	177	0.1872	3140	X-RAY DIFFRACTION	100
3.4928-3.6055	0.2308	166	0.1786	3136	X-RAY DIFFRACTION	100
3.6055-3.7343	0.2246	155	0.1752	3134	X-RAY DIFFRACTION	100
3.7343-3.8838	0.2017	209	0.1569	3092	X-RAY DIFFRACTION	100
3.8838-4.0605	0.2023	145	0.155	3160	X-RAY DIFFRACTION	100
4.0605-4.2746	0.1883	122	0.1467	3168	X-RAY DIFFRACTION	100
4.2746-4.5423	0.1878	185	0.1354	3130	X-RAY DIFFRACTION	100
4.5423-4.8929	0.2262	193	0.139	3103	X-RAY DIFFRACTION	100
4.8929-5.385	0.1986	173	0.1563	3143	X-RAY DIFFRACTION	100
5.385-6.1636	0.2597	141	0.1833	3149	X-RAY DIFFRACTION	100
6.1636-7.763	0.2046	168	0.1788	3135	X-RAY DIFFRACTION	100
7.763-60.9609	0.1716	172	0.1468	3120	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	2.3022	-1.5523	0.0261	4.2803	1.0328	4.0445	-0.1581	-0.2597	-0.1301	0.7818	0.5066	-0.4487	1.3199	0.4994	-0.283	0.8044	0.0716	-0.1182	0.5431	-0.0984	0.3743	33.9727	-70.9577	1.5094
2	4.6391	-0.1106	-0.6766	4.3957	2.3795	3.3417	0.1351	0.2432	0.4305	-0.6226	0.406	-0.9328	-0.8144	0.6208	-0.4324	0.5876	-0.1845	0.2147	0.5634	-0.0651	0.5562	34.0374	-42.7519	-5.0522
3	3.1061	1.4201	1.3239	3.4728	1.3969	4.666	0.1233	-0.5049	0.1179	0.3481	-0.1709	0.1178	0.0052	-0.6013	0.048	0.2439	0.0191	-0.0155	0.4265	-0.0134	0.3141	19.2943	-42.7634	15.5257
4	3.0478	1.1484	-1.0815	2.9586	-0.1608	5.8199	-0.5455	1.0959	-0.0805	-0.7519	0.667	0.3889	1.3333	-1.704	-0.0818	0.948	-0.345	-0.1433	1.3452	0.085	0.4262	-27.0407	-62.0075	-11.0556
5	3.9646	1.6936	-2.0148	5.2125	-2.1433	4.6044	0.0519	0.2676	0.8419	0.0157	0.6642	1.1825	-1.0411	-1.1041	-0.599	0.6832	0.2543	0.0954	0.8611	0.2024	0.6989	-19.7833	-34.8097	-4.496
6	3.083	-0.4708	-1.1092	2.4398	-0.4107	6.4307	0.0139	1.3113	0.2966	-0.6885	0.2705	-0.0311	-0.2691	-0.2661	-0.1494	0.5981	-0.1207	-0.0741	1.2141	0.1162	0.4043	-5.8572	-39.0853	-25.6625

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 202 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 203 through 293 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 294 through 562 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 2 through 202 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 203 through 293 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 294 through 562 )

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