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- PDB-8r48: Structure of plastidial phosphorylase Pho1 from Solanum tuberosum... -

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Basic information

Entry
Database: PDB / ID: 8r48
TitleStructure of plastidial phosphorylase Pho1 from Solanum tuberosum at 2.2 Angstrom resolution
ComponentsAlpha-1,4 glucan phosphorylase L-1 isozyme, chloroplastic/amyloplastic
KeywordsTRANSFERASE / Glycosyltransferase / Carbohydrate metabolism
Function / homology
Function and homology information


amyloplast / glycogen phosphorylase / glycogen phosphorylase activity / glycogen catabolic process / chloroplast / pyridoxal phosphate binding / identical protein binding / cytoplasm
Similarity search - Function
Glycosyl transferase, family 35 / Glycogen/starch/alpha-glucan phosphorylase / Phosphorylase pyridoxal-phosphate attachment site / Carbohydrate phosphorylase / Phosphorylase pyridoxal-phosphate attachment site.
Similarity search - Domain/homology
Alpha-1,4 glucan phosphorylase L-1 isozyme, chloroplastic/amyloplastic
Similarity search - Component
Biological speciesSolanum tuberosum (potato)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å
AuthorsKoulas, S.M. / Leonidas, D.D.
Funding support Greece, 1items
OrganizationGrant numberCountry
Not funded Greece
CitationJournal: 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
DepositionNov 13, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-1,4 glucan phosphorylase L-1 isozyme, chloroplastic/amyloplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,2854
Polymers104,0081
Non-polymers2763
Water5,819323
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


Theoretical massNumber of molelcules
Total (without water)208,5698
Polymers208,0172
Non-polymers5536
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_764-x+2,-x+y+1,-z-2/31
Buried area5960 Å2
ΔGint-23 kcal/mol
Surface area60870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.107, 127.107, 118.693
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 104008.430 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum tuberosum (potato) / References: UniProt: P04045, glycogen phosphorylase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 323 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.94 Å3/Da / Density % sol: 58.14 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris-HCl ph 8.5, 20 % w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.976256 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 30, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976256 Å / Relative weight: 1
ReflectionResolution: 2.24→118.69 Å / Num. obs: 53632 / % possible obs: 100 % / Redundancy: 8.2 % / CC1/2: 0.996 / Rmerge(I) obs: 0.16 / Net I/σ(I): 10.4
Reflection shellResolution: 2.24→2.31 Å / Num. unique obs: 4611 / CC1/2: 0.746

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.24→80.84 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.945 / SU B: 13.946 / SU ML: 0.164 / Cross valid method: THROUGHOUT / ESU R: 0.221 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.22897 2601 4.9 %RANDOM
Rwork0.1759 ---
obs0.17848 50984 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.083 Å2
Baniso -1Baniso -2Baniso -3
1--0.72 Å2-0.36 Å2-0 Å2
2---0.72 Å20 Å2
3---2.34 Å2
Refinement stepCycle: 1 / Resolution: 2.24→80.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6639 0 42 323 7004
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0126830
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9181.6349241
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0125828
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.50422.927369
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.712151182
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6191539
X-RAY DIFFRACTIONr_chiral_restr0.1330.2874
X-RAY DIFFRACTIONr_gen_planes_refined0.010.025230
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.022.8973318
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.1334.3354144
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.0043.163512
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined6.29438.88310397
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.24→2.298 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 188 -
Rwork0.351 3740 -
obs--99.8 %
Refinement TLS params.Method: refined / Origin x: 88.856 Å / Origin y: 42.849 Å / Origin z: -14.608 Å
111213212223313233
T0.0966 Å2-0.0487 Å2-0.03 Å2-0.0852 Å20.0475 Å2--0.1151 Å2
L1.084 °20.1525 °20.0126 °2-0.3077 °2-0.001 °2--0.6092 °2
S0.0705 Å °-0.1816 Å °-0.2191 Å °0.1036 Å °-0.032 Å °-0.0444 Å °0.1651 Å °-0.0204 Å °-0.0385 Å °

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