PDB-5uw1: Activated state yGsy2p in complex with UDP-galactose

ID or keywords:

Entry

Database: PDB / ID: 5uw1

Title

Activated state yGsy2p in complex with UDP-galactose

Components

Glycogen [starch] synthase isoform 2

Keywords

TRANSFERASE / Glycogen Synthase / UDP-Gal / Activated state / complex

Function / homology

Function and homology information

Glycogen synthesis / glycogen binding / glycogen(starch) synthase / alpha-1,4-glucan glucosyltransferase (UDP-glucose donor) activity / glycogen granule / glycogen biosynthetic process / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function

Biological species

Saccharomyces cerevisiae (brewer's yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.26 Å

Authors

Mahalingan, K.K. / Hurley, T.D.

Citation

Journal: To Be Published
Title: Activated state yGsy2p in complex with UDP-galactose
Authors: Mahalingan, K.K. / Hurley, T.D.

History

Deposition	Feb 20, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 28, 2018	Provider: repository / Type: Initial release
Revision 1.1	Jul 29, 2020	Group: Data collection / Derived calculations / Structure summary Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2	Oct 4, 2023	Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5uw1.cif.gz	1014.1 KB	Display	PDBx/mmCIF format
PDB format	pdb5uw1.ent.gz	854.3 KB	Display	PDB format
PDBx/mmJSON format	5uw1.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5uw1_validation.pdf.gz	2.2 MB	Display	wwPDB validaton report
Full document	5uw1_full_validation.pdf.gz	2.3 MB	Display
Data in XML	5uw1_validation.xml.gz	84.2 KB	Display
Data in CIF	5uw1_validation.cif.gz	112.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/uw/5uw1 ftp://data.pdbj.org/pub/pdb/validation_reports/uw/5uw1	HTTPS FTP

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Related structure data

Related structure data	3nb0S 5uw0 5uw4 5uw9 PDB Unreleased entry S: Starting model for refinement
Similar structure data	5uw0-d 5ux7-d 3nb0-d 4kq2-d 4kq1-d 5vnc-d 5uw4-d 4kqm-d 3rt1-d 5suk-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

Deposited unit

A: Glycogen [starch] synthase isoform 2

B: Glycogen [starch] synthase isoform 2

C: Glycogen [starch] synthase isoform 2

D: Glycogen [starch] synthase isoform 2

hetero molecules

331 kDa, 4 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)	193.665, 206.446, 205.099
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	23
Space group name H-M	I222

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D
1	2	A
2	2	B
3	2	C
4	2	D

NCS domain segments:

Refine code: 5

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	SER	SER	GLU	GLU	A	A	2 - 16	22 - 36
2	1	1	SER	SER	GLU	GLU	B	B	2 - 16	22 - 36
3	1	1	SER	SER	GLU	GLU	C	C	2 - 16	22 - 36
4	1	1	SER	SER	GLU	GLU	D	D	2 - 16	22 - 36
1	2	1	ARG	ARG	ASN	ASN	A	A	20 - 50	40 - 70
2	2	1	ARG	ARG	ASN	ASN	B	B	20 - 50	40 - 70
3	2	1	ARG	ARG	ASN	ASN	C	C	20 - 50	40 - 70
4	2	1	ARG	ARG	ASN	ASN	D	D	20 - 50	40 - 70
1	3	1	MET	MET	LEU	LEU	A	A	73 - 125	93 - 145
2	3	1	MET	MET	LEU	LEU	B	B	73 - 125	93 - 145
3	3	1	MET	MET	LEU	LEU	C	C	73 - 125	93 - 145
4	3	1	MET	MET	LEU	LEU	D	D	73 - 125	93 - 145
1	4	1	ASP	ASP	LEU	LEU	A	A	134 - 201	154 - 221
2	4	1	ASP	ASP	LEU	LEU	B	B	134 - 201	154 - 221
3	4	1	ASP	ASP	LEU	LEU	C	C	134 - 201	154 - 221
4	4	1	ASP	ASP	LEU	LEU	D	D	134 - 201	154 - 221
1	5	1	TYR	TYR	PHE	PHE	A	A	228 - 276	248 - 296
2	5	1	TYR	TYR	PHE	PHE	B	B	228 - 276	248 - 296
3	5	1	TYR	TYR	PHE	PHE	C	C	228 - 276	248 - 296
4	5	1	TYR	TYR	PHE	PHE	D	D	228 - 276	248 - 296
1	6	1	LYS	LYS	ASP	ASP	A	A	600 - 620	620 - 640
2	6	1	LYS	LYS	ASP	ASP	B	B	600 - 620	620 - 640
3	6	1	LYS	LYS	ASP	ASP	C	C	600 - 620	620 - 640
4	6	1	LYS	LYS	ASP	ASP	D	D	600 - 620	620 - 640
1	1	2	HIS	HIS	ASP	ASP	A	A	300 - 598	320 - 618
2	1	2	HIS	HIS	ASP	ASP	B	B	300 - 598	320 - 618
3	1	2	HIS	HIS	ASP	ASP	C	C	300 - 598	320 - 618
4	1	2	HIS	HIS	ASP	ASP	D	D	300 - 598	320 - 618

NCS ensembles :

ID
2
1

#1: Protein

Glycogen [starch] synthase isoform 2

Mass: 81818.617 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: GSY2, YLR258W, L8479.8 / Production host:

Escherichia coli (E. coli) / References: UniProt: P27472, glycogen(starch) synthase

#2: Chemical

ChemComp-GDU / GALACTOSE-URIDINE-5'-DIPHOSPHATE / UDP-D-GALACTOPYRANOSE

Mass: 566.302 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C₁₅H₂₄N₂O₁₇P₂

#3: Sugar

ChemComp-G6P / 6-O-phosphono-alpha-D-glucopyranose / ALPHA-D-GLUCOSE-6-PHOSPHATE / 6-O-phosphono-alpha-D-glucose / 6-O-phosphono-D-glucose / 6-O-phosphono-glucose

Type: D-saccharide, alpha linking / Mass: 260.136 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C₆H₁₃O₉P

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.13 Å³/Da / Density % sol: 65.08 %
Crystal grow	Method: vapor diffusion, hanging drop Details: 25 - 30 % Peg 300, 0.1 M Bis-Tris pH 6.1-6.4, 25 mM G-6-P, 10 mM UDP-Gal PH range: 6.1-6.4

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.979 Å
Detector	Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 3, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 3.26→145.5 Å / Num. obs: 63020 / % possible obs: 98.3 % / Redundancy: 4.1 % / Net I/σ(I): 15.3

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0155	refinement
HKL-3000		data reduction
HKL-3000		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3NB0

3nb0

Resolution: 3.26→145.5 Å / Cor.coef. F_o:F_c: 0.948 / Cor.coef. F_o:F_c free: 0.919 / SU B: 50.41 / SU ML: 0.379 / Cross valid method: THROUGHOUT / ESU R Free: 0.451 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23025	3255	5.2 %	RANDOM
R_work	0.18534	-	-	-
obs	0.1877	59712	98.25 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 105.568 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.28 Å²	-0 Å²	0 Å²
2-	-	-4.15 Å²	-0 Å²
3-	-	-	4.43 Å²

Refinement step

Cycle: 1 / Resolution: 3.26→145.5 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	20295	0	208	0	20503

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.019	21004
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	19584
X-RAY DIFFRACTION	r_angle_refined_deg	1.38	1.955	28539
X-RAY DIFFRACTION	r_angle_other_deg	0.95	3	44907
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.298	5	2538
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.227	23.831	1039
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.61	15	3405
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.835	15	136
X-RAY DIFFRACTION	r_chiral_restr	0.073	0.2	3146
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	23801
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	5085
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.988	6.211	10170
X-RAY DIFFRACTION	r_mcbond_other	1.987	6.21	10169
X-RAY DIFFRACTION	r_mcangle_it	3.456	9.313	12702
X-RAY DIFFRACTION	r_mcangle_other	3.456	9.314	12703
X-RAY DIFFRACTION	r_scbond_it	1.849	6.341	10834
X-RAY DIFFRACTION	r_scbond_other	1.849	6.341	10834
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	3.281	9.496	15838
X-RAY DIFFRACTION	r_long_range_B_refined	5.806	71.646	23225
X-RAY DIFFRACTION	r_long_range_B_other	5.806	71.648	23226
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	1392	medium positional	0.21	0.5
1	1	B	1392	medium positional	0.23	0.5
1	1	C	1392	medium positional	0.22	0.5
1	1	D	1392	medium positional	0.22	0.5
2	2	A	1751	medium positional	0.17	0.5
2	2	B	1751	medium positional	0.19	0.5
2	2	C	1751	medium positional	0.22	0.5
2	2	D	1751	medium positional	0.16	0.5
1	1	A	2171	loose positional	0.65	5
1	1	B	2171	loose positional	0.59	5
1	1	C	2171	loose positional	0.62	5
1	1	D	2171	loose positional	0.66	5
2	2	A	2892	loose positional	0.54	5
2	2	B	2892	loose positional	0.53	5
2	2	C	2892	loose positional	0.52	5
2	2	D	2892	loose positional	0.5	5
1	1	A	1392	medium thermal	11.56	2
1	1	B	1392	medium thermal	17.71	2
1	1	C	1392	medium thermal	17.48	2
1	1	D	1392	medium thermal	27.52	2
2	2	A	1751	medium thermal	15.39	2
2	2	B	1751	medium thermal	13.89	2
2	2	C	1751	medium thermal	8.46	2
2	2	D	1751	medium thermal	9.67	2
1	1	A	2171	loose thermal	12.43	10
1	1	B	2171	loose thermal	18.33	10
1	1	C	2171	loose thermal	17.34	10
1	1	D	2171	loose thermal	27.45	10
2	2	A	2892	loose thermal	15.83	10
2	2	B	2892	loose thermal	14.29	10
2	2	C	2892	loose thermal	8.76	10
2	2	D	2892	loose thermal	10.01	10

LS refinement shell

Resolution: 3.263→3.348 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.313	185	-
R_work	0.309	3554	-
obs	-	-	79.64 %

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	2.2491	0.4302	1.0676	0.8811	-0.6797	1.7092	0.4426	0.5122	-0.9863	0.1933	0.0083	-0.4014	-0.1116	0.3671	-0.4509	0.2743	0.0792	-0.0385	0.3003	-0.4988	1.1758	-18.2604	40.7885	-58.6603
2	0.2224	0.27	-0.1399	0.9086	0.058	0.1987	0.0628	-0.0804	-0.0211	0.1219	-0.0355	-0.2046	-0.0083	0.0035	-0.0273	0.3566	-0.0799	-0.3778	0.2923	0.036	0.8102	-37.0375	18.8346	-38.1123
3	2.0748	0.8386	0.242	0.5281	-0.1275	1.8909	-0.4646	0.5473	0.2277	-0.1088	0.3964	0.214	-0.2676	0.4184	0.0682	0.3473	-0.2935	-0.0591	0.7897	0.1013	0.397	-71.7831	-21.5029	-104.5148
4	0.4212	0.1475	0.3012	0.2325	0.2358	0.5029	0.0214	0.1012	-0.1123	0.1144	0.018	-0.0048	0.0455	0.0796	-0.0394	0.3942	0.011	-0.0479	0.3874	0.0118	0.6417	-72.1909	-24.8466	-69.2645
5	1.1905	-0.5827	-0.6504	1.4153	-1.0651	2.0896	-0.4123	0.3367	0.0441	0.9281	-0.1161	-0.6087	-0.6657	-0.2913	0.5284	0.7882	0.0133	-0.5179	0.143	0.0016	0.7603	-27.4675	-42.4354	-30.7732
6	0.2061	-0.3353	0.1102	1.1103	-0.1827	0.1342	-0.0308	0.1407	0.079	0.1255	-0.0296	-0.3077	0.0114	-0.0177	0.0604	0.2372	0.0202	-0.1064	0.3175	0.0969	0.88	-32.3155	-22.3031	-58.4563
7	1.8025	0.8574	0.0182	0.578	-0.5761	2.106	0.167	-0.6345	0.1978	0.0501	-0.112	0.0771	-0.0145	-0.4796	-0.055	0.4123	0.2002	0.3615	0.6783	0.021	0.4203	-93.2591	22.1083	-21.2316
8	0.4285	-0.2931	0.0925	0.4758	-0.0517	0.0317	-0.0426	0.0402	0.1636	0.1217	-0.0293	-0.0212	0.0436	-0.0251	0.072	0.4161	-0.0583	-0.0845	0.3276	-0.0421	0.7219	-73.8253	21.2117	-52.2845

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	2 - 277
2	X-RAY DIFFRACTION	2	A	278 - 639
3	X-RAY DIFFRACTION	3	B	2 - 224
4	X-RAY DIFFRACTION	4	B	225 - 639
5	X-RAY DIFFRACTION	5	C	2 - 276
6	X-RAY DIFFRACTION	6	C	277 - 639
7	X-RAY DIFFRACTION	7	D	2 - 277
8	X-RAY DIFFRACTION	8	D	278 - 639

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