PDB-2bis: Structure of glycogen synthase from Pyrococcus abyssi

ID or keywords:

Entry

Database: PDB / ID: 2bis

Title

Structure of glycogen synthase from Pyrococcus abyssi

Components

GLGA GLYCOGEN SYNTHASE

Keywords

TRANSFERASE / GLYCOSYLTRANSFERASE FAMILY / 5 UDP/ADP-GLUCOSE-GLYCOGEN SYNTHASE / TWO ROSSMAN FOLDS

Function / homology

Function and homology information

alpha-1,4-glucan glucosyltransferase (UDP-glucose donor) activity
Similarity search - Function

Biological species

PYROCOCCUS ABYSSI (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.8 Å

Authors

Horcajada, C. / Guinovart, J.J. / Fita, I. / Ferrer, J.C.

Citation

Journal: J.Biol.Chem. / Year: 2006
Title: Crystal Structure of an Archaeal Glycogen Synthase: Insights Into Oligomerisation and Substrate Binding of Eukaryotic Glycogen Synthases.
Authors: Horcajada, C. / Guinovart, J.J. / Fita, I. / Ferrer, J.C.

History

Deposition	Jan 25, 2005	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 28, 2005	Provider: repository / Type: Initial release
Revision 1.1	May 8, 2011	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 1.3	Jul 29, 2020	Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other / Structure summary Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_unobs_or_zero_occ_residues / struct_conn / struct_site / struct_site_gen Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4	Apr 9, 2025	Group: Advisory / Data collection ...Advisory / 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_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_residues / 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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PDBx/mmCIF format	2bis.cif.gz	264.6 KB	Display	PDBx/mmCIF format
PDB format	pdb2bis.ent.gz	214.3 KB	Display	PDB format
PDBx/mmJSON format	2bis.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bi/2bis ftp://data.pdbj.org/pub/pdb/validation_reports/bi/2bis	HTTPS FTP

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Related structure data

Related structure data	2bfwC C: citing same article (ref.)
Similar structure data	1qjs-2 3d1j-d 3vow-d 4jl5-d 3sr0-d 5m3u-d 3yas-2 5bxv-d 3l01-1 6fi8-1 Search similar-shape structures by Omokage search (details) 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

Related structure data

2bfwC

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#254 - Feb 2021 Cellulose Synthase similarity (2) #156 - Dec 2012 ABO Blood Type Glycosyltransferases similarity (1) #50 - Feb 2004 Glycolytic Enzymes similarity (1) #186 - Jun 2015 Receptor for Advanced Glycation End Products similarity (1) #141 - Sep 2011 O-GlcNAc Transferase similarity (1)

Deposited unit

A: GLGA GLYCOGEN SYNTHASE

B: GLGA GLYCOGEN SYNTHASE

C: GLGA GLYCOGEN SYNTHASE

hetero molecules

150 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: GLGA GLYCOGEN SYNTHASE

hetero molecules

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

2

B: GLGA GLYCOGEN SYNTHASE

hetero molecules

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

3

C: GLGA GLYCOGEN SYNTHASE

hetero molecules

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

Unit cell

Length a, b, c (Å)	202.985, 73.973, 148.221
Angle α, β, γ (deg.)	90.00, 131.19, 90.00
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:

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

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	MET	MET	LEU	LEU	A	A	1 - 11	4 - 14
2	1	1	MET	MET	LEU	LEU	B	B	1 - 11	4 - 14
3	1	1	MET	MET	LEU	LEU	C	C	1 - 11	4 - 14
1	2	1	VAL	VAL	ARG	ARG	A	A	13 - 45	16 - 48
2	2	1	VAL	VAL	ARG	ARG	B	B	13 - 45	16 - 48
3	2	1	VAL	VAL	ARG	ARG	C	C	13 - 45	16 - 48
1	3	1	ARG	ARG	HIS	HIS	A	A	55 - 151	58 - 154
2	3	1	ARG	ARG	HIS	HIS	B	B	55 - 151	58 - 154
3	3	1	ARG	ARG	HIS	HIS	C	C	55 - 151	58 - 154
1	4	1	LEU	LEU	SER	SER	A	A	153 - 169	156 - 172
2	4	1	LEU	LEU	SER	SER	B	B	153 - 169	156 - 172
3	4	1	LEU	LEU	SER	SER	C	C	153 - 169	156 - 172
1	5	1	TYR	TYR	ASN	ASN	A	A	174 - 217	177 - 220
2	5	1	TYR	TYR	ASN	ASN	B	B	174 - 217	177 - 220
3	5	1	TYR	TYR	ASN	ASN	C	C	174 - 217	177 - 220
1	6	1	TRP	TRP	LEU	LEU	A	A	414 - 437	417 - 440
2	6	1	TRP	TRP	LEU	LEU	B	B	414 - 437	417 - 440
3	6	1	TRP	TRP	LEU	LEU	C	C	414 - 437	417 - 440
1	1	2	GLY	GLY	PRO	PRO	A	A	218 - 294	221 - 297
2	1	2	GLY	GLY	PRO	PRO	B	B	218 - 294	221 - 297
3	1	2	GLY	GLY	PRO	PRO	C	C	218 - 294	221 - 297
1	2	2	GLU	GLU	THR	THR	A	A	305 - 314	308 - 317
2	2	2	GLU	GLU	THR	THR	B	B	305 - 314	308 - 317
3	2	2	GLU	GLU	THR	THR	C	C	305 - 314	308 - 317
1	3	2	LEU	LEU	TYR	TYR	A	A	317 - 337	320 - 340
2	3	2	LEU	LEU	TYR	TYR	B	B	317 - 337	320 - 340
3	3	2	LEU	LEU	TYR	TYR	C	C	317 - 337	320 - 340
1	4	2	GLU	GLU	GLU	GLU	A	A	339 - 392	342 - 395
2	4	2	GLU	GLU	GLU	GLU	B	B	339 - 392	342 - 395
3	4	2	GLU	GLU	GLU	GLU	C	C	339 - 392	342 - 395
1	5	2	SER	SER	SER	SER	A	A	396 - 413	399 - 416
2	5	2	SER	SER	SER	SER	B	B	396 - 413	399 - 416
3	5	2	SER	SER	SER	SER	C	C	396 - 413	399 - 416

NCS ensembles :

ID
1
2

NCS oper:

ID	Code	Matrix	Vector
1	given	(-0.245, -0.97, -0.007), (0.462, -0.123, 0.878), (-0.852, 0.212, 0.478)	0.72676, -1.05238, 0.73308
2	given	(-0.32012, 0.44008, -0.83896), (-0.9454, -0.20558, 0.2529), (-0.06118, 0.87411, 0.48186)	0.77712, 0.58377, 0.29646

#1: Protein

GLGA GLYCOGEN SYNTHASE

Mass: 49328.551 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

PYROCOCCUS ABYSSI (archaea) / Plasmid: PET28 / Production host:

ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): (DE3)-RIL
References: UniProt: Q9V2J8, starch synthase (glycosyl-transferring)

#2: Sugar

ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose

Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C₆H₁₂O₆

#3: Chemical

ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE

Mass: 88.105 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C₄H₈O₂

#4: Chemical

ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL

Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₃H₈O₃

#5: Chemical

ChemComp-UDP / URIDINE-5'-DIPHOSPHATE

Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₉H₁₄N₂O₁₂P₂ / Comment: UDP*YM

Has protein modification

Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.7 Å³/Da / Density % sol: 0.55 %
Crystal grow	pH: 5.6 / Details: pH 5.60

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Data collection

Diffraction	Mean temperature: 287 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
Detector	Type: ADSC CCD / Detector: CCD / Details: TOROIDAL MIRROR
Radiation	Monochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.933 Å / Relative weight: 1
Reflection	Resolution: 2.8→29.5 Å / Num. obs: 41024 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 4 % / R_merge(I) obs: 0.09 / Net I/σ(I): 14.1
Reflection shell	Resolution: 2.8→2.9 Å / Redundancy: 4 % / R_merge(I) obs: 0.4 / Mean I/σ(I) obs: 2 / % possible all: 99.8

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0005	refinement
DENZO		data reduction
SCALEPACK		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.8→20 Å / Cor.coef. F_o:F_c: 0.937 / Cor.coef. F_o:F_c free: 0.878 / SU ML: 0.296 / Cross valid method: THROUGHOUT / ESU R Free: 0.395 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.266	2060	5 %	RANDOM
R_work	0.2	-	-	-
obs	0.204	38891	100 %	-

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: 49 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.19 Å²	0 Å²	-1.22 Å²
2-	-	0.75 Å²	0 Å²
3-	-	-	-1.17 Å²

Refinement step

Cycle: LAST / Resolution: 2.8→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10449	0	132	0	10581

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.022	10808
X-RAY DIFFRACTION	r_bond_other_d	0.005	0.02	10038
X-RAY DIFFRACTION	r_angle_refined_deg	1.457	1.974	14542
X-RAY DIFFRACTION	r_angle_other_deg	0.814	3	23284
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.082	5	1315
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.573	23.133	482
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	19.624	15	1860
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.049	15	74
X-RAY DIFFRACTION	r_chiral_restr	0.078	0.2	1567
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	11875
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2352
X-RAY DIFFRACTION	r_nbd_refined	0.211	0.2	2305
X-RAY DIFFRACTION	r_nbd_other	0.197	0.2	10217
X-RAY DIFFRACTION	r_nbtor_refined	0.187	0.2	5209
X-RAY DIFFRACTION	r_nbtor_other	0.091	0.2	6185
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.152	0.2	237
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	0.172	0.2	17
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.203	0.2	46
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.184	0.2	7
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	0.693	1.5	6660
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.925	2	10426
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	1.349	3	4679
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	2.039	4.5	4116
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
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	1326	medium positional	0.19	0.5
1	2	B	1326	medium positional	0.17	0.5
1	3	C	1326	medium positional	0.19	0.5
2	1	A	1057	medium positional	0.29	0.5
2	2	B	1057	medium positional	0.34	0.5
2	3	C	1057	medium positional	0.32	0.5
1	1	A	2192	loose positional	0.51	5
1	2	B	2192	loose positional	0.54	5
1	3	C	2192	loose positional	0.56	5
2	1	A	1682	loose positional	0.76	5
2	2	B	1682	loose positional	0.73	5
2	3	C	1682	loose positional	0.83	5
1	1	A	1326	medium thermal	0.77	2
1	2	B	1326	medium thermal	0.52	2
1	3	C	1326	medium thermal	0.66	2
2	1	A	1057	medium thermal	1.14	2
2	2	B	1057	medium thermal	0.88	2
2	3	C	1057	medium thermal	1.69	2
1	1	A	2192	loose thermal	1.44	10
1	2	B	2192	loose thermal	1.2	10
1	3	C	2192	loose thermal	1.29	10
2	1	A	1682	loose thermal	1.94	10
2	2	B	1682	loose thermal	1.95	10
2	3	C	1682	loose thermal	2.99	10

LS refinement shell

Resolution: 2.8→2.87 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.394	134
R_work	0.296	2822

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