PDB-6uo6: Crystal Structure of the R422Q missense variant of human PGM1

ID or keywords:

Entry

Database: PDB / ID: 6uo6

Title

Crystal Structure of the R422Q missense variant of human PGM1

Components

Phosphoglucomutase-1

PGM1

Keywords

ISOMERASE /

enzyme / missense variant

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 /

MOLECULAR REPLACEMENT / Resolution: 2.15 Å

Authors

Beamer, L.J. / Stiers, K.M.

Funding support

United States, 1items

Citation

Journal: J. Inherit. Metab. Dis. / Year: 2020
Title: A missense variant remote from the active site impairs stability of human phosphoglucomutase 1.
Authors: Stiers, K.M. / Hansen, R.P. / Daghlas, B.A. / Mason, K.N. / Zhu, J.S. / Jakeman, D.L. / Beamer, L.J.

History

Deposition	Oct 14, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 4, 2020	Provider: repository / Type: Initial release
Revision 1.1	Jul 22, 2020	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2	Oct 11, 2023	Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6uo6.cif.gz	544.3 KB	Display	PDBx/mmCIF format
PDB format	pdb6uo6.ent.gz	372.1 KB	Display	PDB format
PDBx/mmJSON format	6uo6.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/uo/6uo6 ftp://data.pdbj.org/pub/pdb/validation_reports/uo/6uo6	HTTPS FTP

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Related structure data

Related structure data	5epcS S: Starting model for refinement
Similar structure data	5jn5-1 3pmg-1 1jdy-2 1lxt-2 5tr2-1 5vg7-1 1vkl-2 5vbi-1 6uiq-1 4qyr-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
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

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

1

A: Phosphoglucomutase-1

hetero molecules

defined by author
Evidence: light scattering
64.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Phosphoglucomutase-1

hetero molecules

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

Unit cell

Length a, b, c (Å)	171.804, 171.804, 99.278
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	92
Space group name H-M	P4₁2₁2
Space group name Hall	P4abw2nw
Symmetry operation	#1: x,y,z #2: -y+1/2,x+1/2,z+1/4 #3: y+1/2,-x+1/2,z+3/4 #4: x+1/2,-y+1/2,-z+3/4 #5: -x+1/2,y+1/2,-z+1/4 #6: -x,-y,z+1/2 #7: y,x,-z #8: -y,-x,-z+1/2

Components on special symmetry positions

ID	Model	Components
1	1	A-1121- HOH

#1: Protein	Phosphoglucomutase-1 / PGM1 / PGM 1 / Glucose phosphomutase 1 Mass: 64162.664 Da / Num. of mol.: 2 / Mutation: R422Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PGM1 / Production host: Escherichia coli (E. coli) 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.: 8 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 625 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.85 Å³/Da / Density % sol: 56.91 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 1.7-1.95 ammonium sulfate, 0.1 M Tris HCl, pH 8.0

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.00003 Å
Detector	Type: RDI CMOS_8M / Detector: CMOS / Date: Dec 11, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.00003 Å / Relative weight: 1
Reflection	Resolution: 2.15→49.61 Å / Num. obs: 80932 / % possible obs: 100 % / Redundancy: 13.9 % / B_iso Wilson estimate: 32.4 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.161 / R_pim(I) all: 0.064 / Χ²: 1.02 / Net I/σ(I): 104.3
Reflection shell	Resolution: 2.15→2.19 Å / Redundancy: 10.6 % / R_merge(I) obs: 1.725 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 4515 / CC_1/2: 0.603 / R_pim(I) all: 0.811 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	1.13_2998	refinement
XDS		data reduction
Aimless		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5epc

5epc

Resolution: 2.15→49.61 Å / SU ML: 0.2489 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.0892

	R_factor	Num. reflection	% reflection
R_free	0.213	4101	5.07 %
R_work	0.1752	-	-
obs	0.1772	80827	99.96 %

Solvent computation

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

Displacement parameters

B_iso mean: 45.04 Å²

Refinement step

Cycle: LAST / Resolution: 2.15→49.61 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8420	0	42	625	9087

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0063	8732
X-RAY DIFFRACTION	f_angle_d	0.78	11875
X-RAY DIFFRACTION	f_chiral_restr	0.0532	1345
X-RAY DIFFRACTION	f_plane_restr	0.0049	1552
X-RAY DIFFRACTION	f_dihedral_angle_d	4.5237	7054

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 (%)
2.15-2.18	0.3383	122	0.27	2615	X-RAY DIFFRACTION	99.96
2.18-2.2	0.2803	128	0.2506	2609	X-RAY DIFFRACTION	99.93
2.2-2.23	0.2903	150	0.2523	2604	X-RAY DIFFRACTION	99.85
2.23-2.26	0.3085	142	0.2624	2601	X-RAY DIFFRACTION	99.89
2.26-2.29	0.2607	148	0.23	2590	X-RAY DIFFRACTION	99.93
2.29-2.32	0.2808	127	0.2171	2651	X-RAY DIFFRACTION	99.96
2.32-2.36	0.2737	135	0.2181	2602	X-RAY DIFFRACTION	99.96
2.36-2.39	0.2645	143	0.2144	2596	X-RAY DIFFRACTION	100
2.39-2.43	0.273	135	0.2143	2636	X-RAY DIFFRACTION	99.96
2.43-2.48	0.268	152	0.2001	2597	X-RAY DIFFRACTION	99.93
2.48-2.52	0.2462	117	0.2068	2640	X-RAY DIFFRACTION	100
2.52-2.57	0.247	133	0.2055	2631	X-RAY DIFFRACTION	100
2.57-2.62	0.2646	149	0.2036	2623	X-RAY DIFFRACTION	100
2.62-2.68	0.2282	138	0.1898	2643	X-RAY DIFFRACTION	99.93
2.68-2.74	0.2211	158	0.1787	2581	X-RAY DIFFRACTION	100
2.74-2.81	0.2087	160	0.1796	2615	X-RAY DIFFRACTION	100
2.81-2.89	0.2277	139	0.1875	2650	X-RAY DIFFRACTION	100
2.89-2.97	0.2315	140	0.1876	2632	X-RAY DIFFRACTION	100
2.97-3.07	0.2522	132	0.1861	2638	X-RAY DIFFRACTION	100
3.07-3.18	0.2214	144	0.1815	2661	X-RAY DIFFRACTION	99.96
3.18-3.3	0.2152	146	0.174	2645	X-RAY DIFFRACTION	99.96
3.3-3.45	0.2012	148	0.1656	2640	X-RAY DIFFRACTION	100
3.45-3.63	0.1904	164	0.1536	2635	X-RAY DIFFRACTION	99.96
3.63-3.86	0.1862	110	0.1393	2702	X-RAY DIFFRACTION	100
3.86-4.16	0.1848	136	0.1443	2692	X-RAY DIFFRACTION	100
4.16-4.58	0.1586	136	0.1308	2678	X-RAY DIFFRACTION	100
4.58-5.24	0.1831	158	0.1344	2707	X-RAY DIFFRACTION	100
5.24-6.6	0.1968	157	0.1822	2732	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	2.73398955334	0.126811788623	0.748478332508	4.79991524086	0.892635635891	2.21554866829	-0.0381629707548	-0.176327182238	-0.125483257331	0.431781927154	0.141910948362	-0.216146864425	0.707048972043	0.206506398801	-0.109776515715	0.540352011616	0.0798751529442	0.00425496423226	0.266561670914	0.0208875534913	0.234786160017	37.626535778	-74.9398786958	8.29292344676
2	0.977757517253	-0.652301889089	-0.163393218415	1.34514601095	0.836905565811	1.76181323663	-0.0102477086307	0.00498263935436	0.0306652389589	-0.0889345683765	0.0808105935653	-0.0547291067786	0.0791046855363	0.036902867661	-0.0552129743951	0.190665754511	-0.0640634281514	0.00729199676065	0.186723406944	0.00221447460844	0.200198248372	28.1903740631	-54.9434961654	-0.0148263816269
3	1.96742235123	0.555889560706	0.5785577529	1.15970723645	0.364357674441	2.36742389776	0.0410633194743	-0.413947237508	0.10964931369	0.106424925211	-0.0945913783491	0.11352784359	-0.0258040937266	-0.357686890875	0.042330885781	0.181294750352	0.0180067288823	-0.0103851843108	0.285228010055	-0.0445428664916	0.251623770812	20.9848067986	-40.5294160661	23.8275845862
4	1.75466902197	-0.3119008352	-1.67330184467	1.80949933226	0.613341129731	4.04366466795	-0.442506043854	-0.493861888752	0.00380483473535	0.86052660901	0.828086850272	0.377998715622	-0.820941051247	-1.07035015087	-0.382838326942	0.653812488375	0.34879680758	0.146789019994	0.956724344827	0.235324697826	0.383619304125	53.9695455068	-22.396824274	-9.48532450202
5	2.31829679164	-1.47252401454	1.13505797567	2.32084065039	-1.53356808556	3.02899296176	-0.0853400681579	-0.484326641044	-0.358455363116	0.135514084535	0.491729466046	0.457361354601	-0.0238592142646	-0.689366279195	-0.233820190579	0.241566939075	-0.0741117358779	0.0352974857722	0.518189180255	0.122711773447	0.29043835951	62.1758456459	-35.5774261974	-17.5098089319
6	1.90393563715	-0.494480598659	0.940270692677	2.88471446282	0.0418125201159	3.91938031785	0.0345994562837	-0.448973022463	-0.0993215908375	0.0940161484535	0.173546494174	0.00376421721242	0.223531439416	-0.0911931541537	-0.158560055498	0.198177328062	-0.0215911792454	0.0034208125891	0.413616735606	0.0213636118442	0.226213796274	79.5043424233	-43.880262953	-10.7435485405
7	1.13509202347	0.110721860992	0.168386033786	2.33233847287	0.620868970716	4.00304063522	0.171851933751	-0.514821266218	-0.175428969524	0.504179035256	-0.0807765188401	0.04735980529	0.58044211247	-0.688436455235	-0.179608618709	0.484398609547	-0.0508997112111	-0.0220669687632	0.742753280663	0.111628345067	0.381750692212	77.3541515528	-51.0164846138	3.83343121855
8	1.9704158726	0.966211922454	-0.668456984849	4.95483726359	0.980095726448	5.43126476533	0.0726150118025	-0.640342434718	-0.335715286381	0.685984500733	0.0500713430148	-0.172821863702	0.501466119003	-0.383270127797	-0.0788849897273	0.503872076398	-0.0641315208218	-0.047440633122	0.839824110674	0.13396164874	0.386744198996	79.7765416446	-48.2619006847	11.1021219232

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid -1 through 52 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 53 through 405 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 406 through 562 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid -1 through 80 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 81 through 278 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 279 through 405 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 406 through 449 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 450 through 562 )

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