PDB-5uw0: Activated state yGsy2p in complex with UDP-2-fluoro-2-deoxy-glucose

ID or keywords:

Entry

Database: PDB / ID: 5uw0

Title

Activated state yGsy2p in complex with UDP-2-fluoro-2-deoxy-glucose

Components

Glycogen [starch] synthase isoform 2

Keywords

TRANSFERASE / UDP-2-fluoro-2-deoxy-glucose / Glycogen Synthase / UDP-glucose

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: 2.73 Å

Authors

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

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: Activated state yGsy2p in complex with UDP-2-fluoro-2-deoxy-glucose
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	Mar 23, 2022	Group: Author supporting evidence / Database references / Structure summary Category: chem_comp / database_2 / pdbx_audit_support Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.3	Oct 4, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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	5uw0.cif.gz	1008.8 KB	Display	PDBx/mmCIF format
PDB format	pdb5uw0.ent.gz	846 KB	Display	PDB format
PDBx/mmJSON format	5uw0.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5uw0_validation.pdf.gz	2.3 MB	Display	wwPDB validaton report
Full document	5uw0_full_validation.pdf.gz	2.3 MB	Display
Data in XML	5uw0_validation.xml.gz	83.6 KB	Display
Data in CIF	5uw0_validation.cif.gz	113 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/uw/5uw0 ftp://data.pdbj.org/pub/pdb/validation_reports/uw/5uw0	HTTPS FTP

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Related structure data

Related structure data	4kqmS 5uw1 5uw4 5uw9 PDB Unreleased entry S: Starting model for refinement
Similar structure data	5uw1-d 5vnc-d 3nb0-d 5uw4-d 3rt1-d 5ux7-d 4kq1-d 4kq2-d 5suk-d 4kqm-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
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

Unit cell

Length a, b, c (Å)	193.516, 204.705, 206.514
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 / Mutation: E169Q
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.: 3
Source method: isolated from a genetically manipulated source
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: obtained synthetically / Formula: C₆H₁₃O₉P

#4: Chemical

ChemComp-U2F / URIDINE-5'-DIPHOSPHATE-2-DEOXY-2-FLUORO-ALPHA-D-GLUCOSE

Mass: 568.293 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C₁₅H₂₃FN₂O₁₆P₂

#5: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 1 / 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: 3.12 Å³/Da / Density % sol: 64.61 %
Crystal grow	Temperature: 298 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-FDG PH range: 6.1-6.5

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Data collection

Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.979 Å
Detector	Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 3, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 2.73→145.38 Å / Num. obs: 102119 / % possible obs: 99.4 % / Redundancy: 4.21 % / CC_1/2: 0.999 / R_merge(I) obs: 0.055 / R_pim(I) all: 0.046 / Net I/σ(I): 11.97

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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: 4KQM

4kqm

Resolution: 2.73→145.38 Å / Cor.coef. F_o:F_c: 0.949 / Cor.coef. F_o:F_c free: 0.939 / SU B: 26.078 / SU ML: 0.239 / Cross valid method: THROUGHOUT / ESU R: 0.56 / ESU R Free: 0.28 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.22449	5465	5.1 %	RANDOM
R_work	0.19876	-	-	-
obs	0.20012	102019	99.49 %	-

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: 80.761 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.61 Å²	-0 Å²	-0 Å²
2-	-	3.75 Å²	-0 Å²
3-	-	-	-1.14 Å²

Refinement step

Cycle: 1 / Resolution: 2.73→145.38 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	20321	0	175	1	20497

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.019	20987
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	19536
X-RAY DIFFRACTION	r_angle_refined_deg	1.384	1.953	28524
X-RAY DIFFRACTION	r_angle_other_deg	0.948	3	44754
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.872	5	2542
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.353	23.776	1046
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.924	15	3384
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.685	15	141
X-RAY DIFFRACTION	r_chiral_restr	0.075	0.2	3137
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	23865
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	5112
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	1.617	5.183	10183
X-RAY DIFFRACTION	r_mcbond_other	1.616	5.182	10182
X-RAY DIFFRACTION	r_mcangle_it	2.82	7.771	12720
X-RAY DIFFRACTION	r_mcangle_other	2.82	7.772	12721
X-RAY DIFFRACTION	r_scbond_it	1.583	5.29	10803
X-RAY DIFFRACTION	r_scbond_other	1.583	5.29	10803
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	2.787	7.918	15805
X-RAY DIFFRACTION	r_long_range_B_refined	4.942	59.345	22828
X-RAY DIFFRACTION	r_long_range_B_other	4.942	59.346	22829
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	0.18	0.5
1	1	B	1392	medium positional	0.19	0.5
1	1	C	1392	medium positional	0.24	0.5
1	1	D	1392	medium positional	0.19	0.5
2	2	A	1763	medium positional	0.15	0.5
2	2	B	1763	medium positional	0.17	0.5
2	2	C	1763	medium positional	0.22	0.5
2	2	D	1763	medium positional	0.14	0.5
1	1	A	2129	loose positional	0.66	5
1	1	B	2129	loose positional	0.65	5
1	1	C	2129	loose positional	0.64	5
1	1	D	2129	loose positional	0.61	5
2	2	A	2976	loose positional	0.58	5
2	2	B	2976	loose positional	0.53	5
2	2	C	2976	loose positional	0.59	5
2	2	D	2976	loose positional	0.55	5
1	1	A	1392	medium thermal	8.57	2
1	1	B	1392	medium thermal	19.11	2
1	1	C	1392	medium thermal	9.21	2
1	1	D	1392	medium thermal	17.66	2
2	2	A	1763	medium thermal	11.54	2
2	2	B	1763	medium thermal	11.69	2
2	2	C	1763	medium thermal	7.74	2
2	2	D	1763	medium thermal	7.74	2
1	1	A	2129	loose thermal	8.98	10
1	1	B	2129	loose thermal	19.5	10
1	1	C	2129	loose thermal	9.69	10
1	1	D	2129	loose thermal	18.1	10
2	2	A	2976	loose thermal	11.91	10
2	2	B	2976	loose thermal	12.14	10
2	2	C	2976	loose thermal	8.16	10
2	2	D	2976	loose thermal	7.99	10

LS refinement shell

Resolution: 2.734→2.805 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.327	366	-
R_work	0.304	7339	-
obs	-	-	97.16 %

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	2.0226	-0.7522	-0.0834	1.3694	1.1031	1.1922	0.3396	0.6605	0.1247	-0.1809	-0.0469	-0.2193	-0.2401	0.3592	-0.2927	0.3477	-0.0255	0.1528	0.7507	0.0376	0.1151	78.9423	59.0771	144.0937
2	0.2235	0.1197	0.2311	0.1999	-0.0465	0.5616	0.0734	0.0451	-0.1087	0.0404	0.0211	-0.0213	0.1102	0.1345	-0.0946	0.2708	0.2648	-0.0941	0.4499	-0.0845	0.1336	60.063	38.6105	121.6258
3	1.4126	-0.5915	0.763	2.7357	-0.2785	0.4434	-0.2073	0.0577	0.5331	0.347	-0.0915	-0.6621	-0.0733	-0.0328	0.2987	0.2942	-0.0109	-0.1871	0.1854	0.0323	0.5117	23.7266	102.7503	79.2926
4	0.4693	-0.4106	0.1959	0.634	-0.2051	0.157	0.0311	0.0905	0.1024	-0.0343	-0.0065	-0.086	0.1043	0.0049	-0.0246	0.3187	0.0321	0.0068	0.3519	-0.0313	0.1491	25.4135	65.7053	79.3685
5	3.4877	0.0835	-0.1793	1.7251	0.7839	0.6712	-0.1758	-0.9645	-0.6556	0.3638	-0.309	0.5281	0.2744	0.1434	0.4848	0.2773	0.1063	0.2527	0.5028	0.247	0.43	64.4604	26.2371	65.7264
6	0.1518	-0.1534	-0.2963	0.2699	0.2189	0.9649	-0.0104	-0.0581	0.0468	-0.0127	0.0088	-0.0076	0.0531	0.2714	0.0016	0.1381	0.0707	0.0157	0.595	-0.0936	0.1008	67.2462	53.4516	74.3222
7	1.7032	1.016	0.3677	3.3906	0.9526	0.2725	-0.0192	-0.5006	-0.6961	-0.3952	-0.0117	0.2849	-0.11	-0.0295	0.0308	0.3869	-0.2164	0.0528	0.2761	0.1995	0.5211	3.8279	20.6908	124.9793
8	0.4839	0.0934	-0.1494	0.0788	0.0543	0.4381	-0.0298	-0.1482	-0.054	-0.0213	0.0582	-0.0469	0.0615	-0.0356	-0.0285	0.3128	0.0659	-0.0386	0.4228	0.0056	0.114	23.311	52.7118	124.2003

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 - 139
6	X-RAY DIFFRACTION	6	C	140 - 639
7	X-RAY DIFFRACTION	7	D	2 - 276
8	X-RAY DIFFRACTION	8	D	277 - 638

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