PDB-8r49: Plastidial phosphorylase Pho1 from Solanum tuberosum in complex w...

ID or keywords:

Entry

Database: PDB / ID: 8r49

Title

Plastidial phosphorylase Pho1 from Solanum tuberosum in complex with beta cyclodextrin

Components

Alpha-1,4 glucan phosphorylase L-1 isozyme, chloroplastic/amyloplastic

Keywords

TRANSFERASE / starch phosphorylase / plastidial phosphorylase / carbohydrate metabolsim

Function / homology

Function and homology information

amyloplast / maltodextrin phosphorylase activity / glycogen phosphorylase / glycogen phosphorylase activity / glycogen catabolic process / chloroplast / pyridoxal phosphate binding / identical protein binding / cytoplasm
Similarity search - Function

Biological species

Solanum tuberosum (potato)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.8 Å

Authors

Koulas, S.M. / Leonidas, D.D.

Funding support

Greece, 1items

Citation

Journal: Acs Omega / Year: 2024
Title: Kinetic and Structural Studies of the Plastidial Solanum tuberosum Phosphorylase.
Authors: Koulas, S.M. / Kyriakis, E. / Tsagkarakou, A.S. / Leonidas, D.D.

History

Deposition	Nov 13, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 9, 2024	Provider: repository / Type: Initial release
Revision 1.1	Oct 23, 2024	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8r49.cif.gz	528.6 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/r4/8r49 ftp://data.pdbj.org/pub/pdb/validation_reports/r4/8r49	HTTPS FTP

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Related structure data

Related structure data	8r48C 8r4gC 8r4jC 8r4kC C: citing same article (ref.)
Similar structure data	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) #155 - Nov 2012 Vitamin D Receptor similarity (1)

Deposited unit

A: Alpha-1,4 glucan phosphorylase L-1 isozyme, chloroplastic/amyloplastic

B: Alpha-1,4 glucan phosphorylase L-1 isozyme, chloroplastic/amyloplastic

C: Alpha-1,4 glucan phosphorylase L-1 isozyme, chloroplastic/amyloplastic

hetero molecules

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

1

A: Alpha-1,4 glucan phosphorylase L-1 isozyme, chloroplastic/amyloplastic

hetero molecules

A: Alpha-1,4 glucan phosphorylase L-1 isozyme, chloroplastic/amyloplastic

hetero molecules

defined by author&software
Evidence: equilibrium centrifugation
211 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Alpha-1,4 glucan phosphorylase L-1 isozyme, chloroplastic/amyloplastic

C: Alpha-1,4 glucan phosphorylase L-1 isozyme, chloroplastic/amyloplastic

hetero molecules

defined by author&software
211 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	218.630, 136.728, 123.155
Angle α, β, γ (deg.)	90.000, 91.470, 90.000
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	A
3	2	A
4	2	A
5	3	A
6	3	A

NCS domain segments:

Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: ALA / End label comp-ID: ALA / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 23 - 916 / Label seq-ID: 23 - 916

Dom-ID	Component-ID	Ens-ID
1	1	1
2	1	1
3	2	2
4	2	2
5	3	3
6	3	3

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6

#1: Protein

Alpha-1,4 glucan phosphorylase L-1 isozyme, chloroplastic/amyloplastic / Starch phosphorylase L-1

Mass: 104008.430 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural)

Solanum tuberosum (potato) / References: UniProt: P04045, glycogen phosphorylase

#2: Polysaccharide

Cycloheptakis-(1-4)-(alpha-D-glucopyranose)

Type: oligosaccharide, Oligosaccharide / Class: Drug delivery / Mass: 1153.001 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: cyclic oligosaccharide / References: beta-cyclodextrin

#3: Chemical

ChemComp-DMS / DIMETHYL SULFOXIDE

Mass: 78.133 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C₂H₆OS / Comment: DMSO, precipitant*YM

#4: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H₂O

Has ligand of interest

Y

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: 2.96 Å³/Da / Density % sol: 58.38 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M Tris-HCl, 20 % PEG4000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.976256 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 26, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.976256 Å / Relative weight: 1
Reflection	Resolution: 2.8→123.114 Å / Num. obs: 87204 / % possible obs: 98 % / Redundancy: 3 % / CC_1/2: 0.995 / R_merge(I) obs: 0.09 / Net I/σ(I): 7.4
Reflection shell	Resolution: 2.8→2.85 Å / R_merge(I) obs: 0.818 / Num. unique obs: 4507 / CC_1/2: 0.654

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0419	refinement
XDS		data reduction
Aimless		data scaling
REFMAC		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.8→123.114 Å / Cor.coef. F_o:F_c: 0.949 / Cor.coef. F_o:F_c free: 0.942 / WR_factor R_free: 0.239 / WR_factor R_work: 0.224 / SU B: 19.3 / SU ML: 0.332 / Average fsc free: 0.9443 / Average fsc work: 0.951 / Cross valid method: THROUGHOUT / ESU R: 2.486 / ESU R Free: 0.34
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.239	4411	5.059 %	RANDOM
R_work	0.2176	82781	-	-
all	0.219	-	-	-
obs	-	87192	97.836 %	-

Solvent computation

Ion probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 88.194 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.278 Å²	0 Å²	1.78 Å²
2-	-	6.759 Å²	0 Å²
3-	-	-	-4.566 Å²

Refinement step

Cycle: LAST / Resolution: 2.8→123.114 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	20010	0	263	101	20374

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.003	0.012	20742
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	19428
X-RAY DIFFRACTION	r_angle_refined_deg	1.077	1.835	28089
X-RAY DIFFRACTION	r_angle_other_deg	0.402	1.764	44841
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.518	5	2478
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	5.871	5	126
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.186	10	3555
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	13.361	10	993
X-RAY DIFFRACTION	r_chiral_restr	0.092	0.2	3101
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	24156
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	4779
X-RAY DIFFRACTION	r_nbd_refined	0.222	0.2	4954
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.196	0.2	19110
X-RAY DIFFRACTION	r_nbtor_refined	0.18	0.2	10193
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.075	0.2	10382
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.182	0.2	403
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.029	0.2	5
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.106	0.2	17
X-RAY DIFFRACTION	r_nbd_other	0.143	0.2	107
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.093	0.2	13
X-RAY DIFFRACTION	r_mcbond_it	2.324	8.818	9954
X-RAY DIFFRACTION	r_mcbond_other	2.324	8.818	9954
X-RAY DIFFRACTION	r_mcangle_it	3.858	15.858	12414
X-RAY DIFFRACTION	r_mcangle_other	3.858	15.858	12415
X-RAY DIFFRACTION	r_scbond_it	2.098	9.157	10788
X-RAY DIFFRACTION	r_scbond_other	2.098	9.157	10789
X-RAY DIFFRACTION	r_scangle_it	3.662	16.829	15675
X-RAY DIFFRACTION	r_scangle_other	3.662	16.829	15676
X-RAY DIFFRACTION	r_lrange_it	7.763	106.229	89181
X-RAY DIFFRACTION	r_lrange_other	7.763	106.234	89171
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.088	0.05	28169
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.101	0.05	27875
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.102	0.05	27794

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.08795	0.05011
1	2	A	X-RAY DIFFRACTION	Local ncs	0.08795	0.05011
2	3	A	X-RAY DIFFRACTION	Local ncs	0.1007	0.05011
2	4	A	X-RAY DIFFRACTION	Local ncs	0.1007	0.05011
3	5	A	X-RAY DIFFRACTION	Local ncs	0.10154	0.05011
3	6	A	X-RAY DIFFRACTION	Local ncs	0.10154	0.05011

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.8-2.873	0.363	301	0.377	6239	0.376	6582	0.894	0.889	99.3619	0.374
2.873-2.951	0.379	293	0.357	5976	0.358	6344	0.911	0.906	98.8178	0.349
2.951-3.037	0.392	285	0.339	5859	0.342	6226	0.899	0.918	98.6829	0.33
3.037-3.13	0.389	282	0.319	5601	0.322	6045	0.907	0.93	97.3201	0.306
3.13-3.233	0.344	274	0.305	5551	0.307	5880	0.922	0.938	99.0646	0.291
3.233-3.346	0.289	281	0.283	5294	0.283	5658	0.943	0.948	98.5331	0.269
3.346-3.472	0.343	282	0.272	5151	0.276	5495	0.923	0.953	98.8717	0.26
3.472-3.614	0.288	232	0.262	4951	0.264	5267	0.951	0.957	98.4052	0.252
3.614-3.775	0.253	225	0.234	4741	0.235	5049	0.96	0.967	98.3561	0.226
3.775-3.959	0.271	247	0.222	4462	0.225	4811	0.954	0.97	97.8799	0.216
3.959-4.173	0.22	227	0.2	4290	0.201	4638	0.971	0.975	97.3911	0.196
4.173-4.425	0.207	241	0.179	3965	0.18	4356	0.974	0.98	96.5565	0.18
4.425-4.731	0.212	225	0.166	3719	0.169	4098	0.973	0.983	96.2421	0.172
4.731-5.109	0.204	205	0.168	3509	0.17	3809	0.974	0.983	97.5059	0.174
5.109-5.596	0.214	200	0.189	3224	0.19	3525	0.977	0.981	97.1348	0.197
5.596-6.255	0.225	155	0.202	2928	0.203	3183	0.972	0.979	96.8583	0.21
6.255-7.219	0.237	168	0.193	2566	0.196	2837	0.973	0.98	96.3694	0.204
7.219-8.834	0.168	130	0.147	2143	0.148	2384	0.982	0.987	95.344	0.161
8.834-12.461	0.14	101	0.131	1683	0.131	1870	0.991	0.991	95.4011	0.15
12.461-123.114	0.165	57	0.245	928	0.24	1063	0.983	0.958	92.6623	0.573

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