PDB-4bqe: Arabidopsis thaliana Cytosolic Alpha-1,4-glucan Phosphorylase (PHS2)

ID or keywords:

Entry

Database: PDB / ID: 4bqe

Title

Arabidopsis thaliana Cytosolic Alpha-1,4-glucan Phosphorylase (PHS2)

Components

ALPHA-GLUCAN PHOSPHORYLASE 2,4-GLUCAN PHOSPHORYLASE

Keywords

TRANSFERASE / TRANSFERASEE / INHIBITORS / CARBOHYDRATE METABOLISM / ALPHA-1 / SELF-ASSEMBLY ON SURFACES / SURFACE PLASMON RESONANCE / GOLD NANOPARTICLES

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 / glycogen catabolic process / chloroplast / pyridoxal phosphate binding / cytosol
Similarity search - Function

Biological species

ARABIDOPSIS THALIANA (thale cress)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.7 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 1.2	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4bqe.cif.gz	699.6 KB	Display	PDBx/mmCIF format
PDB format	pdb4bqe.ent.gz	573.9 KB	Display	PDB format
PDBx/mmJSON format	4bqe.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4bqe_validation.pdf.gz	495.4 KB	Display	wwPDB validaton report
Full document	4bqe_full_validation.pdf.gz	505.5 KB	Display
Data in XML	4bqe_validation.xml.gz	75.8 KB	Display
Data in CIF	4bqe_validation.cif.gz	117.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bq/4bqe ftp://data.pdbj.org/pub/pdb/validation_reports/bq/4bqe	HTTPS FTP

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Related structure data

Related structure data	4bqfC 4bqiC 1gpbS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4bqi-d 6y55-1 5lrf-1 1wv1-1 3mrv-1 2c4m-1 5owy-1 1gpy-1 5owz-1 1l5r-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	#24 - Dec 2001 Glycogen Phosphorylase similarity (6)

Deposited unit

A: ALPHA-GLUCAN PHOSPHORYLASE 2,4-GLUCAN PHOSPHORYLASE

B: ALPHA-GLUCAN PHOSPHORYLASE 2,4-GLUCAN PHOSPHORYLASE

hetero molecules

199 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)	84.670, 117.100, 94.180
Angle α, β, γ (deg.)	90.00, 106.72, 90.00
Int Tables number	4
Space group name H-M	P12₁1

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Protein , 1 types, 2 molecules AB

#1: Protein	ALPHA-GLUCAN PHOSPHORYLASE 2,4-GLUCAN PHOSPHORYLASE / ATPHS2 / ALPHA-GLUCAN PHOSPHORYLASE / H ISOZYME / STARCH PHOSPHORYLASE H / ATPHS2 / ALPHA-GLUCAN ...ATPHS2 / ALPHA-GLUCAN PHOSPHORYLASE / H ISOZYME / STARCH PHOSPHORYLASE H / ATPHS2 / ALPHA-GLUCAN PHOSPHORYLASE / H ISOZYME 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 PLYSS / References: UniProt: Q9SD76, glycogen phosphorylase

#1: Protein

ALPHA-GLUCAN PHOSPHORYLASE 2,4-GLUCAN PHOSPHORYLASE / ATPHS2 / ALPHA-GLUCAN PHOSPHORYLASE / H ISOZYME / STARCH PHOSPHORYLASE H / ATPHS2 / ALPHA-GLUCAN ...

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 PLYSS / References: UniProt: Q9SD76, glycogen phosphorylase

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Non-polymers , 5 types, 1853 molecules

#2: Chemical	ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₈H₁₀NO₆P
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#5: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1844 / Source method: isolated from a natural source / Formula: H₂O

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Details

Nonpolymer details	PYRIDOXAL-5'-PHOSPHATE (PLP): COVALENTLY LINKED TO LYS 687 OF CORRESPONDING PROTEIN CHAIN
Sequence details	A 33-RESIDUE HEXAHISTIDINE AFFINITY TAG IS APPENDED TO THE N-TERMINUS OF THE WILD-TYPE SEQUENCE AND ...A 33-RESIDUE HEXAHISTIDINE AFFINITY TAG IS APPENDED TO THE N-TERMINUS OF THE WILD-TYPE SEQUENCE AND IS DERIVED FROM THE PET151 EXPRESSION VECTOR

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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: I03 / Wavelength: 0.971
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 2, 2010
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.971 Å / Relative weight: 1
Reflection	Resolution: 1.7→49.11 Å / Num. obs: 190517 / % possible obs: 98.9 % / Observed criterion σ(I): 0 / Redundancy: 4.2 % / B_iso Wilson estimate: 17.8 Å² / R_merge(I) obs: 0.08 / Net I/σ(I): 11.8
Reflection shell	Resolution: 1.7→1.79 Å / Redundancy: 3.2 % / R_merge(I) obs: 0.43 / Mean I/σ(I) obs: 2.5 / % possible all: 93.5

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GPB

1gpb

Resolution: 1.7→90.2 Å / Cor.coef. F_o:F_c: 0.97 / Cor.coef. F_o:F_c free: 0.957 / SU B: 3.442 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.18274	9587	5 %	RANDOM
R_work	0.15278	-	-	-
obs	0.15427	180900	98.86 %	-

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: 19.2 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.25 Å²	0 Å²	0.06 Å²
2-	-	0.16 Å²	0 Å²
3-	-	-	-0.37 Å²

Refinement step

Cycle: LAST / Resolution: 1.7→90.2 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13065	0	79	1844	14988

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.02	13663
X-RAY DIFFRACTION	r_bond_other_d	0.004	0.02	9323
X-RAY DIFFRACTION	r_angle_refined_deg	1.486	1.958	18573
X-RAY DIFFRACTION	r_angle_other_deg	1.055	3.001	22641
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.748	5	1712
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.059	24.165	653
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.856	15	2320
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.519	15	92
X-RAY DIFFRACTION	r_chiral_restr	0.09	0.2	2030
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.021	15296
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	2844
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: 1.7→1.744 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.284	641	-
R_work	0.267	12079	-
obs	-	-	90.05 %

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	3.4447	0.0538	0.7995	4.1216	2.237	3.3896	0.0622	-0.1086	-0.2032	0.0284	0.0872	0.0329	0.1792	0.0464	-0.1494	0.0536	-0.0102	-0.0304	0.0169	0.0335	0.09	40.7473	-41.8399	48.5472
2	0.6121	0.0772	0.1946	0.6867	0.0398	0.5536	0.0067	-0.0147	-0.1074	0.0481	0.0478	-0.0334	0.0256	0.0249	-0.0546	0.0164	-0.0022	0.0032	0.0284	-0.0221	0.0416	43.5065	-26.3478	31.763
3	3.0028	0.6654	3.2024	0.2051	0.4654	4.5326	-0.1595	0.2194	0.0591	-0.0317	0.0564	-0.0106	-0.2426	0.2012	0.1031	0.0592	-0.0125	0.0295	0.0258	0.0004	0.06	51.6122	-5.4231	41.3753
4	0.6037	1.0884	0.0786	2.0359	-0.2007	1.8019	-0.1189	0.0862	-0.0875	-0.2068	0.1173	-0.1587	-0.06	0.0983	0.0017	0.0595	-0.0451	0.0408	0.0969	-0.0389	0.0306	53.1666	-16.9906	16.7761
5	1.6982	1.3406	0.0632	1.6257	0.1713	0.4198	-0.1689	0.2263	0.098	-0.3121	0.1839	0.0775	-0.1401	0.0582	-0.015	0.1017	-0.0308	-0.0064	0.0663	-0.0074	0.0183	38.5723	-16.031	11.7751
6	0.4885	0.0128	0.286	2.2728	0.7143	0.787	-0.0077	-0.0853	-0.0399	0.1181	-0.0281	0.0996	0.0312	-0.1531	0.0359	0.0169	0.0003	0.0116	0.0554	-0.0021	0.0184	10.2321	-22.2661	29.9701
7	0.734	-0.3627	0.0621	1.1469	0.1356	1.083	0.0363	0.0508	0.1016	-0.1418	-0.0636	0.0692	-0.1759	-0.1249	0.0273	0.0461	0.0161	-0.0065	0.0432	-0.011	0.0416	11.3732	-13.6681	23.2176
8	2.956	1.3425	-0.1624	0.7628	-0.1763	0.6432	-0.0464	0.4407	-0.0034	-0.1178	0.1618	-0.0124	0.0037	0.0903	-0.1154	0.0714	0.0053	0.0211	0.0889	-0.0177	0.0265	31.964	-33.0375	13.221
9	3.3293	-0.4519	1.0656	4.4815	-1.5627	3.6788	0.0328	0.0841	-0.1781	-0.0062	0.0487	0.0419	0.1513	0.0943	-0.0815	0.0333	0.0301	-0.0278	0.0522	-0.069	0.105	58.9376	-41.2081	43.1606
10	0.4884	-0.0661	0.1219	0.6386	0.0843	0.5478	0.0253	0.0759	-0.1107	-0.0556	-0.007	-0.0164	0.0538	0.0427	-0.0182	0.0161	0.0022	-0.0053	0.0199	-0.0082	0.0381	55.0669	-26.3466	60.4484
11	3.4373	0.0026	3.6766	0.0515	0.0575	4.8711	-0.1047	-0.1988	0.11	0.0031	-0.0276	0.0529	-0.1834	-0.1803	0.1323	0.0363	0.0034	0.0144	0.0269	-0.0315	0.0639	45.2996	-5.9105	51.0026
12	0.6575	-1.0542	0.0877	1.7065	-0.0166	1.7945	-0.0637	-0.0199	-0.0542	0.1101	0.0157	0.0882	0.0203	-0.0526	0.048	0.0156	-0.0105	0.0042	0.0196	0.0042	0.0077	45.1682	-17.4619	75.31
13	1.1649	-0.6227	-0.11	0.8598	0.1382	0.4266	-0.0626	-0.1118	-0.006	0.1235	0.0634	-0.0493	0.0392	0.0619	-0.0008	0.0315	-0.0037	-0.0189	0.0311	0.0125	0.0148	64.3625	-20.0248	77.323
14	0.6279	0.6367	0.1638	1.6163	-0.4926	1.0499	0.011	0.026	-0.005	0.0912	-0.0786	-0.1379	-0.0887	0.2176	0.0676	0.0203	-0.0237	-0.017	0.0924	0.0339	0.0345	85.8923	-15.4091	62.9494
15	0.7142	0.3854	-0.0074	2.1807	-0.7153	0.8024	0.0662	-0.0768	0.1455	0.435	-0.1393	-0.1001	-0.2966	0.1954	0.073	0.1534	-0.0716	-0.0456	0.1521	0.021	0.0751	88.6723	-8.7538	73.5601
16	2.2398	-1.5284	-0.1879	1.0558	0.212	0.739	-0.1167	-0.2355	-0.0046	0.1103	0.1472	-0.0032	0.1967	0.0367	-0.0305	0.1207	-0.0129	-0.0066	0.0532	0.0259	0.0429	61.8506	-32.645	79.5461

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	15 - 58
2	X-RAY DIFFRACTION	2	A	59 - 250
3	X-RAY DIFFRACTION	3	A	251 - 296
4	X-RAY DIFFRACTION	4	A	297 - 387
5	X-RAY DIFFRACTION	5	A	388 - 526
6	X-RAY DIFFRACTION	6	A	527 - 624
7	X-RAY DIFFRACTION	7	A	625 - 805
8	X-RAY DIFFRACTION	8	A	806 - 841
9	X-RAY DIFFRACTION	9	B	15 - 58
10	X-RAY DIFFRACTION	10	B	59 - 250
11	X-RAY DIFFRACTION	11	B	251 - 294
12	X-RAY DIFFRACTION	12	B	295 - 389
13	X-RAY DIFFRACTION	13	B	390 - 556
14	X-RAY DIFFRACTION	14	B	557 - 704
15	X-RAY DIFFRACTION	15	B	705 - 812
16	X-RAY DIFFRACTION	16	B	813 - 841

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Protein , 1 types, 2 molecules AB

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Non-polymers , 5 types, 1853 molecules

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Details

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