PDB-4ueg: Crystal structure of human glycogenin-2 catalytic domain

ID or keywords:

Entry

Database: PDB / ID: 4ueg

Title

Crystal structure of human glycogenin-2 catalytic domain

Components

GLYCOGENIN-2

Keywords

TRANSFERASE / GLYCOGEN BIOSYNTHESIS /

GLYCOSYLATION

Function / homology

Function and homology information

Glycogen storage disease type 0 (liver GYS2) / Glycogen storage disease type IV (GBE1) /

glycogenin glucosyltransferase /

glycogenin glucosyltransferase activity / UDP-alpha-D-glucose:glucosyl-glycogenin alpha-D-glucosyltransferase activity / glycogen biosynthetic process / Glycogen breakdown (glycogenolysis) /

Glycogen synthesis /

metal ion binding /

cytosol /

cytoplasm
Similarity search - Function

Biological species

HOMO SAPIENS (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.93 Å

Authors

Fairhead, M. / Strain-Damerell, C. / Krojer, T. / Froese, D.S. / Kopec, J. / Nowak, R. / Burgess-Brown, N. / von Delft, F. / Arrowsmith, C. / Edwards, A. ...

Citation

Journal: To be Published
Title: Crystal Structure of Human Glycogenin-2 Catalytic Domain
Authors: Fairhead, M. / Strain-Damerell, C. / Krojer, T. / Froese, D.S. / Kopec, J. / Nowak, R. / Burgess-Brown, N. / von Delft, F. / Arrowsmith, C. / Edwards, A. / Bountra, C. / Yue, W.W.

History

Deposition	Dec 17, 2014	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 24, 2014	Provider: repository / Type: Initial release
Revision 1.1	Jan 24, 2018	Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.2	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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 / _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	4ueg.cif.gz	217.5 KB	Display	PDBx/mmCIF format
PDB format	pdb4ueg.ent.gz	175.2 KB	Display	PDB format
PDBx/mmJSON format	4ueg.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/ue/4ueg ftp://data.pdbj.org/pub/pdb/validation_reports/ue/4ueg	HTTPS FTP

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Related structure data

Related structure data	3q4sS S: Starting model for refinement
Similar structure data	5tpb-d 3q37-d 3ews-d 1dwq-1 4mwa-1 1bl3-1 1xg5-2 3nzr-d 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) #156 - Dec 2012 ABO Blood Type Glycosyltransferases similarity (1) #60 - Dec 2004 Ubiquitin similarity (1) #254 - Feb 2021 Cellulose Synthase 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: GLYCOGENIN-2

B: GLYCOGENIN-2

hetero molecules

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

1

A: GLYCOGENIN-2

B: GLYCOGENIN-2

hetero molecules

A: GLYCOGENIN-2

B: GLYCOGENIN-2

hetero molecules

defined by author&software
132 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	127.113, 80.541, 73.683
Angle α, β, γ (deg.)	90.00, 118.74, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	GLYCOGENIN-2 / / GN-2 / GN2 / GLYCOGENIN-2 CATALYTIC DOMAIN Mass: 33100.340 Da / Num. of mol.: 2 / Fragment: GLYCOSYLTRANSFERASE, RESIDUES 35-300 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC-CTHF / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2 / References: UniProt: O15488, glycogenin glucosyltransferase
#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 255 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	ARTIFICIAL CONSTRUCT ENCODING CATALYTIC DOMAIN OF HUMAN GLYCOGENIN-2 AND A C-TERMINAL HISTIDINE TAG

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.65 Å³/Da / Density % sol: 53.68 % / Description: NONE
Crystal grow	pH: 8.5 Details: 0.3 M MGFORMATE, 0.1 M TRIS PH 8.5 WITH 30 % ETHYLENE GLYCOL IN MOTHER LIQUOR AS CRYOPROTECTANT

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

Diamond

/ Beamline: I03 / Wavelength: 0.6, 2.3

Detector

Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 20, 2014

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.6	1
2	2.3	1

Reflection

Resolution: 1.93→64.61 Å / Num. obs: 47488 / % possible obs: 96.8 % / Observed criterion σ(I): 2 / Redundancy: 5.2 % / B_iso Wilson estimate: 33.63 Å² / R_merge(I) obs: 0.06 / Net I/σ(I): 14.91

Reflection shell

Resolution: 1.93→2 Å / Redundancy: 5.3 % / R_merge(I) obs: 0.74 / Mean I/σ(I) obs: 2.31 / % possible all: 95.4

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
XDS		data reduction
SCALEPACK		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3Q4S

3q4s

Resolution: 1.93→64.608 Å / SU ML: 0.23 / σ(F): 1.88 / Phase error: 27.05 / Stereochemistry target values: ML
Details: DISORDERED LOOPS AND SIDECHAINS WERE OMITTED FROM THE STRUCTURE.

	R_factor	Num. reflection	% reflection
R_free	0.2243	2248	4.8 %
R_work	0.1867	-	-
obs	0.1885	47356	96.58 %

Solvent computation

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

Displacement parameters

B_iso mean: 44.5 Å²

Refinement step

Cycle: LAST / Resolution: 1.93→64.608 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3921	0	2	255	4178

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	4077
X-RAY DIFFRACTION	f_angle_d	0.84	5559
X-RAY DIFFRACTION	f_dihedral_angle_d	13.323	1405
X-RAY DIFFRACTION	f_chiral_restr	0.034	625
X-RAY DIFFRACTION	f_plane_restr	0.004	699

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 (%)
1.9299-1.9719	0.3725	145	0.3188	2715	X-RAY DIFFRACTION	94
1.9719-2.0178	0.3173	123	0.2733	2800	X-RAY DIFFRACTION	96
2.0178-2.0682	0.3309	131	0.2572	2782	X-RAY DIFFRACTION	96
2.0682-2.1241	0.2885	121	0.2368	2836	X-RAY DIFFRACTION	97
2.1241-2.1866	0.2551	144	0.2202	2815	X-RAY DIFFRACTION	97
2.1866-2.2572	0.3839	147	0.28	2573	X-RAY DIFFRACTION	90
2.2572-2.3379	0.2587	126	0.2334	2737	X-RAY DIFFRACTION	93
2.3379-2.4315	0.2457	147	0.2012	2841	X-RAY DIFFRACTION	98
2.4315-2.5422	0.2394	141	0.1913	2851	X-RAY DIFFRACTION	97
2.5422-2.6762	0.2401	178	0.1949	2799	X-RAY DIFFRACTION	98
2.6762-2.8439	0.2285	127	0.1956	2867	X-RAY DIFFRACTION	98
2.8439-3.0635	0.217	139	0.1907	2872	X-RAY DIFFRACTION	98
3.0635-3.3717	0.2331	165	0.1843	2874	X-RAY DIFFRACTION	98
3.3717-3.8596	0.195	131	0.1686	2873	X-RAY DIFFRACTION	98
3.8596-4.8624	0.1502	140	0.1479	2906	X-RAY DIFFRACTION	99
4.8624-64.6441	0.2172	143	0.1687	2967	X-RAY DIFFRACTION	99

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	0.3726	-0.1122	0.1928	0.2289	0.1014	0.2202	0.1215	-0.0146	0.1699	0.2353	0.0429	0.0236	-0.3628	-0.0697	-0.0004	0.4295	-0.0523	0.0423	0.3664	-0.0272	0.3017	7.917	55.6799	27.4914
2	1.2751	0.5725	0.6182	0.601	-0.1297	0.9389	0.1548	-0.5571	0.0184	0.0855	-0.0103	-0.0367	-0.3795	0.4397	0.0015	0.4179	-0.0573	0.0407	0.4306	-0.05	0.3101	12.2594	58.1019	28.2483
3	0.5472	0.314	-0.1325	0.2982	0.0139	0.0906	0.0566	-0.111	-0.3187	-0.2366	0.0051	-0.066	0.2135	0.1574	-0	0.3512	0.1012	-0.0449	0.2426	0.0259	0.3848	11.509	42.5229	17.5272
4	1.3373	0.3817	0.2324	0.8452	0.5057	0.2952	0.1436	-0.2833	-0.0977	-0.0077	-0.0097	0.1331	-0.2452	-0.1874	-0.0002	0.3495	0.0368	0.0118	0.3385	0.0285	0.2936	-3.2668	52.6332	25.2117
5	0.7599	0.4564	-0.1193	0.4435	0.1867	0.4153	0.173	0.1502	-0.3636	-0.341	-0.0866	-0.1491	0.1649	0.1606	-0.0001	0.3952	0.0651	-0.0287	0.2748	0.0002	0.4597	2.6468	40.9483	15.8884
6	0.6759	0.2816	0.0907	0.3647	-0.1338	0.134	-0.0134	-0.2379	-0.171	0.0421	0.1057	0.3908	0.1469	-0.4306	0.0001	0.3542	0.035	-0.0076	0.4165	0.0272	0.4076	-11.236	51.619	20.3074
7	0.6723	0.3712	0.1231	0.2336	0.002	0.1309	-0.386	0.5846	0.1742	-0.2354	0.2221	0.531	-0.4514	-0.076	-0.0085	0.7583	-0.0208	-0.0363	0.4398	0.0033	0.4939	-3.3244	67.4825	16.757
8	1.7192	-0.1536	-0.6126	0.0464	0.1484	0.5258	0.4968	0.0573	1.0406	-0.0936	-0.016	-0.2093	-0.7759	0.0882	0.5972	0.8705	-0.0126	0.1208	0.3343	-0.0785	0.5499	4.0928	73.4998	22.8131
9	-0.0002	-0.0008	-0.0026	0.099	0.1248	0.1547	0.1221	-0.194	0.1202	0.0887	0.1323	-0.2272	0.0291	0.1131	0.6127	0.9239	-0.306	0.0894	0.5379	-0.2278	0.5144	18.1932	71.4765	29.4323
10	0.543	0.0915	0.1098	0.2599	-0.1591	0.4589	0.1553	-0.4634	-0.0421	0.0394	-0.0301	-0.0332	-0.1254	0.2552	-0.0001	0.3802	-0.0973	0.033	0.5077	-0.0028	0.3793	33.5031	52.447	3.9683
11	0.3042	-0.2507	0.2384	0.1994	-0.2097	0.6857	0.3352	-0.4712	-0.0748	0.3127	-0.1305	-0.2811	-0.2318	0.4187	0.0068	0.347	-0.0808	-0.0069	0.4194	0.0094	0.3589	37.4996	51.3538	2.4069
12	0.617	-0.3911	-0.5261	0.364	0.3165	0.4585	0.0765	-0.4988	0.0245	0.3999	-0.0231	-0.3234	-0.0406	0.8176	0.0715	0.395	-0.1483	-0.0513	0.7123	-0.0034	0.4494	43.2149	57.0641	5.3622
13	1.6908	0.184	-0.2213	0.6907	-0.2879	0.9588	0.1303	-0.0313	0.0912	-0.0194	-0.0697	-0.0095	-0.1732	0.1341	-0	0.3448	-0.074	0.0251	0.3452	-0.0538	0.3519	32.807	56.6251	-9.212
14	0.3072	0.0646	0.0753	0.6536	-0.0024	0.4462	0.3302	0.0061	0.3003	-0.2814	-0.0805	-0.0463	-0.3543	0.2137	-0.0002	0.4662	-0.1185	0.0905	0.4114	-0.0405	0.3986	34.0344	64.5664	-16.5733
15	0.3694	0.2985	0.2298	0.3003	0.1049	0.2252	-0.0649	0.3612	-0.3602	-0.3008	0.1056	-0.092	0.2058	0.1963	0.0002	0.44	-0.1005	0.001	0.4513	-0.0419	0.4118	22.4819	50.8055	-16.7
16	0.0055	-0.0063	-0.0148	-0.0006	0.0143	0.0925	-0.036	-0.4558	0.552	0.7405	-0.0976	0.7144	-0.1343	-0.5181	-0.0005	0.6311	-0.0621	0.1263	0.5947	-0.1501	0.675	11.2577	55.472	-0.0596
17	0.2142	0.044	0.2106	0.1344	0.0987	0.2251	-0.3356	-0.5468	-0.4966	-0.195	0.2693	0.2548	-0.0538	-0.0515	0.0002	0.417	-0.0309	0.0104	0.5155	0.0616	0.5354	12.5134	47.6099	-1.722
18	0.1169	0.07	0.0309	0.2577	-0.1498	0.1377	0.2904	-0.4029	0.4509	0.1562	-0.0432	0.0679	-0.7818	0.2088	-0.0001	0.5958	-0.0719	0.0411	0.4822	-0.0178	0.468	19.3556	62.3881	8.9671
19	0.3821	-0.0448	-0.3722	0.3406	0.0543	0.3529	0.2312	-0.477	0.1375	-0.0267	-0.0537	0.3506	-0.1594	-0.0272	0.0001	0.3761	-0.0468	0.0169	0.5633	-0.0282	0.3705	23.2929	52.2949	13.2999

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'A' AND (RESID 4 THROUGH 16 )
2	X-RAY DIFFRACTION	2	CHAIN 'A' AND (RESID 17 THROUGH 69 )
3	X-RAY DIFFRACTION	3	CHAIN 'A' AND (RESID 70 THROUGH 93 )
4	X-RAY DIFFRACTION	4	CHAIN 'A' AND (RESID 94 THROUGH 144 )
5	X-RAY DIFFRACTION	5	CHAIN 'A' AND (RESID 145 THROUGH 172 )
6	X-RAY DIFFRACTION	6	CHAIN 'A' AND (RESID 173 THROUGH 200 )
7	X-RAY DIFFRACTION	7	CHAIN 'A' AND (RESID 201 THROUGH 245 )
8	X-RAY DIFFRACTION	8	CHAIN 'A' AND (RESID 246 THROUGH 259 )
9	X-RAY DIFFRACTION	9	CHAIN 'A' AND (RESID 260 THROUGH 269 )
10	X-RAY DIFFRACTION	10	CHAIN 'B' AND (RESID 4 THROUGH 30 )
11	X-RAY DIFFRACTION	11	CHAIN 'B' AND (RESID 31 THROUGH 46 )
12	X-RAY DIFFRACTION	12	CHAIN 'B' AND (RESID 47 THROUGH 69 )
13	X-RAY DIFFRACTION	13	CHAIN 'B' AND (RESID 70 THROUGH 144 )
14	X-RAY DIFFRACTION	14	CHAIN 'B' AND (RESID 145 THROUGH 172 )
15	X-RAY DIFFRACTION	15	CHAIN 'B' AND (RESID 173 THROUGH 189 )
16	X-RAY DIFFRACTION	16	CHAIN 'B' AND (RESID 190 THROUGH 200 )
17	X-RAY DIFFRACTION	17	CHAIN 'B' AND (RESID 201 THROUGH 214 )
18	X-RAY DIFFRACTION	18	CHAIN 'B' AND (RESID 215 THROUGH 242 )
19	X-RAY DIFFRACTION	19	CHAIN 'B' AND (RESID 243 THROUGH 265 )

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