PDB-4bqi: ARABIDOPSIS THALIANA cytosolic alpha-1,4-glucan phosphorylase (PH...

ID or keywords:

Entry

Database: PDB / ID: 4bqi

Title

ARABIDOPSIS THALIANA cytosolic alpha-1,4-glucan phosphorylase (PHS2) in complex with maltotriose

Components

ALPHA-GLUCAN PHOSPHORYLASE 2, CYTOSOLIC

Keywords

TRANSFERASE /

CARBOHYDRATE METABOLISM / SELF-ASSEMBLY ON SURFACES

Function / homology

Function and homology information

1,4-alpha-oligoglucan phosphorylase activity / response to water deprivation /

glycogen phosphorylase /

glycogen phosphorylase activity / linear malto-oligosaccharide phosphorylase activity / SHG alpha-glucan phosphorylase activity /

chloroplast /

pyridoxal phosphate binding / carbohydrate metabolic process /

cytosol
Similarity search - Function

Biological species

ARABIDOPSIS THALIANA (thale cress)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

O'Neill, E.C. / Rashid, A.M. / Stevenson, C.E.M. / Hetru, A.C. / Gunning, A.P. / Rejzek, M. / Nepogodiev, S.A. / Bornemann, S. / Lawson, D.M. / Field, R.A.

Citation

Journal: Chem.Sci. / Year: 2014
Title: Sugar-Coated Sensor Chip and Nanoparticle Surfaces for the in Vitro Enzymatic Synthesis of Starch-Like Materials
Authors: O'Neill, E.C. / Rashid, A.M. / Stevenson, C.E.M. / Hetru, A.C. / Gunning, A.P. / Rejzek, M. / Nepogodiev, S.A. / Bornemann, S. / Lawson, D.M. / Field, R.A.

History

Deposition	May 30, 2013	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 19, 2014	Provider: repository / Type: Initial release
Revision 1.1	May 8, 2019	Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol / struct_conn Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp ..._exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0	Jul 29, 2020	Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Other / Structure summary Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_asym / struct_conn / struct_site / struct_site_gen Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _pdbx_database_status.status_code_sf / _struct_asym.entity_id Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1	Dec 20, 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 Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4bqi.cif.gz	671.7 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bq/4bqi ftp://data.pdbj.org/pub/pdb/validation_reports/bq/4bqi	HTTPS FTP

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Related structure data

Related structure data	4bqeC 4bqfC 1gpbS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4bqe-d 2c4m-2 6y55-1 6s4o-1 1wv1-1 5lrf-1 2c4m-1 3ebp-1 1gpy-1 3cem-d 2qnb-1 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	#24 - Dec 2001 Glycogen Phosphorylase similarity (6)

Deposited unit

A: ALPHA-GLUCAN PHOSPHORYLASE 2, CYTOSOLIC

B: ALPHA-GLUCAN PHOSPHORYLASE 2, CYTOSOLIC

hetero molecules

200 kDa, 2 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)	83.713, 116.072, 94.342
Angle α, β, γ (deg.)	90.00, 107.38, 90.00
Int Tables number	4
Space group name H-M	P12₁1

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein

ALPHA-GLUCAN PHOSPHORYLASE 2, CYTOSOLIC / ATPHS2 / ALPHA-GLUCAN PHOSPHORYLASE / H ISOZYME / STARCH PHOSPHORYLASE H / PHS2

Mass: 99064.359 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

ARABIDOPSIS THALIANA (thale cress) / Plasmid: PET151-PHS2 / Production host:

ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA-2 LYSSS / References: UniProt: Q9SD76,

glycogen phosphorylase

#2: Polysaccharide

alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltotriose

Type: oligosaccharide

, Oligosaccharide

/ Class: Nutrient

/ Mass: 504.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltotriose

Descriptor	Type	Program
DGlcpa1-4DGlcpa1-4DGlcpa1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/1,3,2/[a2122h-1a_1-5]/1-1-1/a4-b1_b4-c1	WURCS	PDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}	LINUCS	PDB-CARE

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Non-polymers , 4 types, 923 molecules

#3: Chemical	ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₈H₁₀NO₆P
#4: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 919 / Source method: isolated from a natural source / Formula: H₂O

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Details

Nonpolymer details	MALTOTRIOSE (MLR): CRYSTAL WAS SOAKED FOR 1 WEEK IN A 1 MILLIMOLAR SOLUTION OF MALTOTRIOSE MADE UP ...MALTOTRIOSE (MLR): CRYSTAL WAS SOAKED FOR 1 WEEK IN A 1 MILLIMOLAR SOLUTION OF MALTOTRIOSE MADE UP IN CRYSTALLIZATION WELL SOLUTION PYRIDOXAL-5'-PHOSPHATE (PLP): COVALENTLY LINKED TO LYS 687 OF CORRESPONDING PROTEIN CHAIN

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.26 Å³/Da / Density % sol: 45.6 % / Description: NONE
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.25 Details: CRYSTALLISED FROM APPROXIMATELY 20% PEG3350, 100 MM AMMONIUM CITRATE PH 8.25, 10% GLYCEROL USING THE HANGING DROP VAPOUR DIFFUSION METHOD AT 20 DEG C. 1 MICROLITRE OF PROTEIN AT 10 MG PER ML ...Details: CRYSTALLISED FROM APPROXIMATELY 20% PEG3350, 100 MM AMMONIUM CITRATE PH 8.25, 10% GLYCEROL USING THE HANGING DROP VAPOUR DIFFUSION METHOD AT 20 DEG C. 1 MICROLITRE OF PROTEIN AT 10 MG PER ML IN 12.5 MM HEPES PH 7.5, 25 MM NACL WAS MIXED WITH 1 MICROLITRE OF THE WELL SOLUTION TO GIVE THE FINAL DROP

Crystal

Density Matthews: 2.26 Å³/Da / Density % sol: 45.6 % / Description: NONE

Crystal grow

Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.25
Details: CRYSTALLISED FROM APPROXIMATELY 20% PEG3350, 100 MM AMMONIUM CITRATE PH 8.25, 10% GLYCEROL USING THE HANGING DROP VAPOUR DIFFUSION METHOD AT 20 DEG C. 1 MICROLITRE OF PROTEIN AT 10 MG PER ML ...

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.98
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 15, 2011
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.98 Å / Relative weight: 1
Reflection	Resolution: 1.9→65.81 Å / Num. obs: 132861 / % possible obs: 98.2 % / Observed criterion σ(I): 0 / Redundancy: 4 % / B_iso Wilson estimate: 28.1 Å² / R_merge(I) obs: 0.06 / Net I/σ(I): 12.9
Reflection shell	Resolution: 1.9→2 Å / Redundancy: 3.4 % / R_merge(I) obs: 0.56 / Mean I/σ(I) obs: 2.2 / % possible all: 88.8

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Processing

Software

Name	Version	Classification
REFMAC	5.6.0117	refinement
XDS		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GPB

1gpb

Resolution: 1.9→52.48 Å / Cor.coef. F_o:F_c: 0.952 / Cor.coef. F_o:F_c free: 0.93 / SU B: 8.076 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.171 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.24106	6643	5 %	RANDOM
R_work	0.19576	-	-	-
obs	0.19799	126128	98.19 %	-

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: 33.2 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.95 Å²	0 Å²	-1.04 Å²
2-	-	-0.81 Å²	0 Å²
3-	-	-	-0.75 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→52.48 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12957	0	111	919	13987

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.02	13472
X-RAY DIFFRACTION	r_bond_other_d	0.005	0.02	9079
X-RAY DIFFRACTION	r_angle_refined_deg	1.545	1.961	18330
X-RAY DIFFRACTION	r_angle_other_deg	1.155	3	22091
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.164	5	1674
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.389	24.188	628
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.604	15	2222
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.275	15	85
X-RAY DIFFRACTION	r_chiral_restr	0.093	0.2	2033
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.021	15035
X-RAY DIFFRACTION	r_gen_planes_other	0.004	0.02	2786
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
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
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

LS refinement shell

Resolution: 1.9→1.949 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.352	439	-
R_work	0.287	7793	-
obs	-	-	83.79 %

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	3.6995	1.6074	1.8939	9.1062	5.3712	7.5451	0.0286	-0.0549	-0.4014	-0.1763	-0.0166	0.0311	0.329	0.0567	-0.012	0.0782	0.0093	-0.0241	0.03	0.047	0.1295	41.4961	-43.8492	48.0936
2	1.4316	0.2028	-0.7598	1.045	-0.5344	1.7313	-0.0034	-0.0203	-0.2064	0.0685	-0.0155	-0.024	0.1926	0.1554	0.0189	0.0533	0.0307	-0.0243	0.0376	-0.0281	0.0589	41.7292	-34.6243	31.9267
3	0.4049	-0.0174	0.2157	1.2795	0.0141	0.6241	0.0436	-0.0277	-0.0913	0.1335	-0.0368	-0.0008	0.0522	0.0466	-0.0068	0.0263	0.0076	-0.011	0.0624	-0.0033	0.0282	42.6496	-23.0585	33.2448
4	0.3817	0.331	0.2726	0.7639	-0.1252	0.8414	-0.044	0.1255	0.0536	-0.0776	0.0015	-0.0273	-0.1062	0.1397	0.0424	0.0381	0.0035	0.0145	0.1166	0.0112	0.0411	47.2737	-10.6548	17.7767
5	1.3944	0.0652	-0.1907	2.2265	1.0074	1.1516	0.0546	-0.1396	-0.0764	0.2706	-0.011	0.066	0.1969	0.0232	-0.0436	0.073	-0.007	0.0077	0.0146	0.0072	0.0266	15.3056	-36.1775	26.0384
6	0.9295	-0.0594	0.3778	1.657	-0.0819	1.5813	-0.0074	-0.0282	0.2176	0.0863	-0.0298	0.262	-0.1308	-0.1513	0.0372	0.0225	0.0025	0.0257	0.0255	-0.0191	0.1109	10.3519	-13.124	25.5085
7	1.6369	1.7852	-0.8121	10.6002	-1.3368	1.1136	0.1338	0.0595	0.3501	0.2671	-0.0959	0.5882	-0.1094	-0.0328	-0.0379	0.028	0.0087	0.0144	0.045	-0.0007	0.1169	7.069	-12.0668	19.2034
8	3.1684	1.9168	-0.9141	1.2068	-0.6282	0.3849	-0.0359	0.3134	0.1461	-0.0814	0.1125	0.1067	0.1007	0.0359	-0.0766	0.0949	0.0763	-0.0105	0.171	-0.0294	0.0258	30.6958	-32.8469	13.4053
9	2.8938	-0.5733	0.631	3.6479	-0.1322	4.4879	0.064	0.2961	-0.195	-0.1394	-0.0552	-0.0722	0.1714	0.0578	-0.0088	0.0671	0.0296	-0.0178	0.0688	-0.0282	0.1194	57.5013	-40.7261	44.3816
10	0.4686	-0.0521	0.0095	0.9251	0.0819	0.7821	0.0363	0.0451	-0.1263	-0.0746	-0.0725	-0.0491	0.0228	0.1053	0.0362	0.0389	-0.016	-0.021	0.0529	0.016	0.0515	54.1301	-25.9289	60.8089
11	4.5849	-1.8844	6.1106	3.5227	-5.0372	10.505	-0.0855	-0.1737	0.2309	0.1789	0.0012	0.1135	-0.2931	-0.1479	0.0843	0.0889	-0.0104	0.0357	0.0267	-0.0348	0.0552	39.1782	-6.2112	46.5491
12	0.9632	-0.3093	-0.1728	1.451	0.1447	1.691	-0.0139	-0.1695	0.0461	0.1916	-0.0325	0.0188	-0.0886	0.02	0.0465	0.0349	-0.0123	-0.0011	0.0494	-0.0007	0.0115	45.713	-11.7072	76.3993
13	0.9775	-0.4581	0.0473	0.9433	0.0845	0.5295	-0.0243	-0.0293	-0.0892	0.0075	0.0389	-0.1133	0.0626	0.1614	-0.0145	0.0825	-0.0386	-0.0401	0.1038	0.046	0.084	71.5939	-25.3158	73.2261
14	1.0959	0.2126	0.6629	1.8424	0.0984	1.2263	-0.1256	0.0609	0.1241	-0.0724	0.0657	-0.2207	-0.278	0.2824	0.0599	0.116	-0.0987	-0.0147	0.2277	0.0525	0.1099	85.1801	-11.3775	66.9893
15	1.9877	-2.1502	0.0673	10.0564	1.1576	1.8368	-0.1137	-0.0371	0.2908	0.0001	0.1108	-0.5573	-0.2409	0.1769	0.003	0.0977	-0.111	-0.0388	0.2589	0.0172	0.0941	89.5773	-11.7173	72.8191
16	2.0853	-1.5722	-0.7543	1.3332	0.8269	0.7354	-0.0845	-0.3808	0.0061	0.1582	0.2135	-0.0843	0.2034	0.0552	-0.129	0.1338	-0.0246	-0.0494	0.1528	0.0893	0.0998	65.8113	-32.799	78.8667

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	15 - 47
2	X-RAY DIFFRACTION	2	A	48 - 108
3	X-RAY DIFFRACTION	3	A	109 - 253
4	X-RAY DIFFRACTION	4	A	254 - 495
5	X-RAY DIFFRACTION	5	A	496 - 573
6	X-RAY DIFFRACTION	6	A	574 - 767
7	X-RAY DIFFRACTION	7	A	768 - 805
8	X-RAY DIFFRACTION	8	A	806 - 841
9	X-RAY DIFFRACTION	9	B	15 - 63
10	X-RAY DIFFRACTION	10	B	64 - 250
11	X-RAY DIFFRACTION	11	B	251 - 278
12	X-RAY DIFFRACTION	12	B	279 - 430
13	X-RAY DIFFRACTION	13	B	431 - 571
14	X-RAY DIFFRACTION	14	B	572 - 767
15	X-RAY DIFFRACTION	15	B	768 - 806
16	X-RAY DIFFRACTION	16	B	807 - 841

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-Protein / Sugars , 2 types, 4 molecules AB

-Non-polymers , 4 types, 923 molecules

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Movie

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Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

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Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein / Sugars , 2 types, 4 molecules AB

-
Non-polymers , 4 types, 923 molecules

-
Details

-
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

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Yorodumi