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- PDB-8r4k: Plastidial phosphorylase Pho1 trimer from Solanum tuberosum -

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Basic information

Entry
Database: PDB / ID: 8r4k
TitlePlastidial phosphorylase Pho1 trimer from Solanum tuberosum
ComponentsAlpha-1,4 glucan phosphorylase L-1 isozyme, chloroplastic/amyloplastic
KeywordsTRANSFERASE / plastidial phosphorylase / 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: 3.3 Å
AuthorsKoulas, S.M. / Leonidas, D.D.
Funding support1items
OrganizationGrant numberCountry
Not funded
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 16, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)312,1174
Polymers312,0253
Non-polymers921
Water1,13563
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)208,2014
Polymers208,0172
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area5240 Å2
ΔGint-25 kcal/mol
Surface area60050 Å2
MethodPISA
2
B: Alpha-1,4 glucan phosphorylase L-1 isozyme, chloroplastic/amyloplastic

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


Theoretical massNumber of molelcules
Total (without water)208,0172
Polymers208,0172
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area4800 Å2
ΔGint-25 kcal/mol
Surface area60180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)218.058, 134.907, 123.105
Angle α, β, γ (deg.)90.00, 91.30, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEILEAA23 - 91523 - 915
21ILEILEBB23 - 91523 - 915
12ALAALAAA23 - 91623 - 916
22ALAALACC23 - 91623 - 916
13ILEILEBB23 - 91523 - 915
23ILEILECC23 - 91523 - 915

NCS ensembles :
ID
1
2
3

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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.: 3 / 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.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.91 Å3/Da / Density % sol: 57.69 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M Tris-HCl, 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: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 20, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 3.3→123.07 Å / Num. obs: 52489 / % possible obs: 97.9 % / Redundancy: 3 % / CC1/2: 0.997 / Net I/σ(I): 9.5
Reflection shellResolution: 3.3→3.4 Å / Num. unique obs: 4606 / CC1/2: 0.805

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→123.07 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.886 / SU B: 40.243 / SU ML: 0.59 / Cross valid method: THROUGHOUT / ESU R Free: 0.644 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.30038 2539 4.8 %RANDOM
Rwork0.25439 ---
obs0.25653 49944 97.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.21 Å2
Baniso -1Baniso -2Baniso -3
1--8.25 Å20 Å22.7 Å2
2--11.35 Å20 Å2
3----3.22 Å2
Refinement stepCycle: 1 / Resolution: 3.3→123.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19920 0 78 63 20061
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01220471
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2681.63427713
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1752486
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.94222.9241108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.471153548
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.01915117
X-RAY DIFFRACTIONr_chiral_restr0.090.22624
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215729
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A295750.04
12B295750.04
21A295460.03
22C295460.03
31B294380.04
32C294380.04
LS refinement shellResolution: 3.3→3.386 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.417 211 -
Rwork0.392 3752 -
obs--99.27 %

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