PDB-5ux7: Activated state yeast Glycogen Synthase in complex with UDP-xylose

ID or keywords:

Entry

Database: PDB / ID: 5ux7

Title

Activated state yeast Glycogen Synthase in complex with UDP-xylose

Components

Glycogen [starch] synthase isoform 2

Keywords

TRANSFERASE / Glycogen Synthase / UDP-xylose / complex / sugar

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: 2.69 Å

Authors

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

Citation

Journal: To Be Published
Title: Activated state yeast Glycogen Synthase in complex with UDP-xylose
Authors: Mahalingan, K.K. / Hurley, T.D.

History

Deposition	Feb 22, 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	Mar 6, 2024	Group: Data collection / Database references / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5ux7.cif.gz	1011.4 KB	Display	PDBx/mmCIF format
PDB format	pdb5ux7.ent.gz	849.3 KB	Display	PDB format
PDBx/mmJSON format	5ux7.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	5ux7_validation.pdf.gz	2.6 MB	Display	wwPDB validaton report
Full document	5ux7_full_validation.pdf.gz	2.6 MB	Display
Data in XML	5ux7_validation.xml.gz	82.8 KB	Display
Data in CIF	5ux7_validation.cif.gz	112.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ux/5ux7 ftp://data.pdbj.org/pub/pdb/validation_reports/ux/5ux7	HTTPS FTP

-
Related structure data

Similar structure data	4kq2-d 4kq1-d 5uw1-d 5uw4-d 3nb0-d 5uw0-d 4kqm-d 6u77-d 5suk-d 3rt1-d 5vnc-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

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#156 - Dec 2012 ABO Blood Type Glycosyltransferases similarity (1) #254 - Feb 2021 Cellulose Synthase similarity (1) #141 - Sep 2011 O-GlcNAc Transferase similarity (1)

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

330 kDa, 4 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)	192.993, 204.322, 206.674
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:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	5	A	1 - 16
2	1	1	5	B	1 - 16
3	1	1	5	C	1 - 16
4	1	1	5	D	1 - 16
1	2	1	5	A	20 - 50
2	2	1	5	B	20 - 50
3	2	1	5	C	20 - 50
4	2	1	5	D	20 - 50
1	3	1	5	A	73 - 125
2	3	1	5	B	73 - 125
3	3	1	5	C	73 - 125
4	3	1	5	D	73 - 125
1	4	1	5	A	134 - 201
2	4	1	5	B	134 - 201
3	4	1	5	C	134 - 201
4	4	1	5	D	134 - 201
1	5	1	5	A	228 - 276
2	5	1	5	B	228 - 276
3	5	1	5	C	228 - 276
4	5	1	5	D	228 - 276
1	6	1	5	A	600 - 620
2	6	1	5	B	600 - 620
3	6	1	5	C	600 - 620
4	6	1	5	D	600 - 620
1	1	2	5	A	300 - 598
2	1	2	5	B	300 - 598
3	1	2	5	C	300 - 598
4	1	2	5	D	300 - 598

NCS ensembles :

ID
2
1

#1: Protein

Glycogen [starch] synthase isoform 2

Mass: 81819.602 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-UDP / URIDINE-5'-DIPHOSPHATE

Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₉H₁₄N₂O₁₂P₂ / Comment: UDP*YM

#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

#4: Chemical

ChemComp-UDX / URIDINE-5'-DIPHOSPHATE-XYLOPYRANOSE / UDP-ALPHA-D-XYLOPYRANOSE

Mass: 536.276 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₄H₂₂N₂O₁₆P₂

#5: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 3.11 Å³/Da / Density % sol: 64.82 %
Crystal grow	Temperature: 293 K / 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-xylose PH range: 6.1-6.4

-
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: 2.69→145.5 Å / Num. obs: 105353 / % possible obs: 98.3 % / Redundancy: 3.9 % / Net I/σ(I): 20.1

-
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 / Resolution: 2.69→145.3 Å / Cor.coef. F_o:F_c: 0.944 / Cor.coef. F_o:F_c free: 0.919 / SU B: 26.576 / SU ML: 0.253 / Cross valid method: THROUGHOUT / ESU R: 0.544 / ESU R Free: 0.3 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.24622	5559	5 %	RANDOM
R_work	0.2075	-	-	-
obs	0.20942	105353	98.27 %	-

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: 79.441 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.28 Å²	-0 Å²	-0 Å²
2-	-	3.41 Å²	-0 Å²
3-	-	-	-1.13 Å²

Refinement step

Cycle: 1 / Resolution: 2.69→145.3 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	20465	0	182	1	20648

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.019	21150
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	19832
X-RAY DIFFRACTION	r_angle_refined_deg	1.309	1.954	28709
X-RAY DIFFRACTION	r_angle_other_deg	0.927	3	45480
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.899	5	2545
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.458	23.661	1057
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.734	15	3489
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.071	15	150
X-RAY DIFFRACTION	r_chiral_restr	0.071	0.2	3142
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	23935
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	5147
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	1.568	5.456	10195
X-RAY DIFFRACTION	r_mcbond_other	1.567	5.456	10194
X-RAY DIFFRACTION	r_mcangle_it	2.764	8.18	12735
X-RAY DIFFRACTION	r_mcangle_other	2.764	8.181	12736
X-RAY DIFFRACTION	r_scbond_it	1.413	5.584	10955
X-RAY DIFFRACTION	r_scbond_other	1.413	5.584	10955
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	2.515	8.346	15975
X-RAY DIFFRACTION	r_long_range_B_refined	4.68	62.354	23049
X-RAY DIFFRACTION	r_long_range_B_other	4.68	62.354	23049
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	1398	medium positional	0.22	0.5
1	1	B	1398	medium positional	0.18	0.5
1	1	C	1398	medium positional	0.19	0.5
1	1	D	1398	medium positional	0.19	0.5
2	2	A	1757	medium positional	0.16	0.5
2	2	B	1757	medium positional	0.17	0.5
2	2	C	1757	medium positional	0.2	0.5
2	2	D	1757	medium positional	0.16	0.5
1	1	A	2313	loose positional	0.66	5
1	1	B	2313	loose positional	0.62	5
1	1	C	2313	loose positional	0.58	5
1	1	D	2313	loose positional	0.62	5
2	2	A	2939	loose positional	0.57	5
2	2	B	2939	loose positional	0.53	5
2	2	C	2939	loose positional	0.55	5
2	2	D	2939	loose positional	0.53	5
1	1	A	1398	medium thermal	8.22	2
1	1	B	1398	medium thermal	13.48	2
1	1	C	1398	medium thermal	10.67	2
1	1	D	1398	medium thermal	22.15	2
2	2	A	1757	medium thermal	9.81	2
2	2	B	1757	medium thermal	11.66	2
2	2	C	1757	medium thermal	8.74	2
2	2	D	1757	medium thermal	7.04	2
1	1	A	2313	loose thermal	8.6	10
1	1	B	2313	loose thermal	13.87	10
1	1	C	2313	loose thermal	11.12	10
1	1	D	2313	loose thermal	22.26	10
2	2	A	2939	loose thermal	10.35	10
2	2	B	2939	loose thermal	12.3	10
2	2	C	2939	loose thermal	9.11	10
2	2	D	2939	loose thermal	7.34	10

LS refinement shell

Resolution: 2.691→2.76 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.361	366	-
R_work	0.315	7169	-
obs	-	-	90.9 %

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	1.6752	0.0788	-0.4221	1.0431	-0.4394	0.2929	0.1856	0.483	-0.1732	-0.1523	-0.1057	0.315	0.0623	-0.105	-0.0799	0.2177	0.0499	-0.0281	0.4269	-0.1955	0.1948	-79.0257	-58.8485	41.1756
2	0.256	0.1277	-0.2777	0.1576	-0.0015	0.5691	0.0728	0.0176	0.1364	0.0317	0.018	0.0597	-0.0912	-0.0563	-0.0908	0.188	0.1856	0.1059	0.3404	0.0576	0.1803	-59.8547	-38.3102	18.7292
3	1.4175	-0.6344	-0.6986	2.4043	0.2342	0.3856	-0.294	0.1022	-0.6273	0.3886	-0.0321	0.5707	0.0813	0.0035	0.3261	0.3071	-0.0228	0.1899	0.1512	-0.0265	0.4721	-23.8141	-102.4386	-23.5766
4	0.5761	-0.3028	-0.2233	0.4424	0.182	0.15	0.0122	0.101	-0.0935	-0.0317	0.004	0.0594	-0.0741	-0.0084	-0.0163	0.258	0.0072	-0.0152	0.3275	0.0303	0.1222	-25.4058	-65.4503	-23.7658
5	0.5567	0.0693	0.7545	1.1595	0.0775	1.0261	-0.2521	-0.2678	0.2234	0.1837	-0.0574	-0.1075	-0.3465	-0.336	0.3094	0.3546	0.1655	-0.1702	0.3384	-0.1099	0.1145	-67.2991	-27.4449	-41.5075
6	0.1444	-0.214	0.2122	0.3558	-0.2617	0.7702	0.0155	-0.0104	-0.0719	-0.025	0.0056	0.0895	0.0166	-0.1721	-0.0211	0.0943	0.0037	-0.0592	0.4715	0.087	0.1353	-66.1074	-56.203	-26.0444
7	3.453	0.0828	-0.6674	2.3686	-1.0378	0.5811	0.1705	-0.1876	1.0597	-0.1715	-0.1258	-0.3578	0.0834	0.0436	-0.0448	0.164	-0.1653	-0.0018	0.2491	-0.0142	0.5574	-3.6487	-20.6054	21.4174
8	0.5423	0.1344	0.0892	0.0923	0.0126	0.3528	-0.0385	-0.1717	0.0569	-0.0291	0.0567	0.0604	-0.0173	0.0675	-0.0182	0.2246	0.0598	0.0318	0.4215	0.0096	0.0823	-23.1725	-51.9464	21.0262

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	2 - 275
2	X-RAY DIFFRACTION	2	A	276 - 639
3	X-RAY DIFFRACTION	3	B	2 - 275
4	X-RAY DIFFRACTION	4	B	276 - 639
5	X-RAY DIFFRACTION	5	C	2 - 214
6	X-RAY DIFFRACTION	6	C	215 - 639
7	X-RAY DIFFRACTION	7	D	2 - 275
8	X-RAY DIFFRACTION	8	D	276 - 639

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi