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- PDB-8r4j: Plastidial phosphorylase Pho1 from Solanum tuberosum in complex w... -

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Basic information

Entry
Database: PDB / ID: 8r4j
TitlePlastidial phosphorylase Pho1 from Solanum tuberosum in complex with caffeine
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
CAFFEINE / Alpha-1,4 glucan phosphorylase L-1 isozyme, chloroplastic/amyloplastic
Similarity search - Component
Biological speciesSolanum tuberosum (potato)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.7 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 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
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)312,4967
Polymers312,0253
Non-polymers4704
Water32418
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)208,3856
Polymers208,0172
Non-polymers3684
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area5070 Å2
ΔGint-25 kcal/mol
Surface area61270 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)208,3034
Polymers208,0172
Non-polymers2862
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5330 Å2
ΔGint-23 kcal/mol
Surface area61320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)218.828, 136.093, 123.193
Angle α, β, γ (deg.)90.00, 91.55, 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 / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 23 - 916 / Label seq-ID: 23 - 916

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13BB
23CC

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.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CFF / CAFFEINE / 3,7-DIHYDRO-1,3,7-TRIMETHYL-1H-PURINE-2,6-DIONE


Mass: 194.191 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10N4O2 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 58.23 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 / 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: Jun 26, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976256 Å / Relative weight: 1
ReflectionResolution: 3.7→49.54 Å / Num. obs: 37747 / % possible obs: 98 % / Redundancy: 3 % / CC1/2: 0.947 / Net I/σ(I): 3.3
Reflection shellResolution: 3.7→3.86 Å / Num. unique obs: 4635 / CC1/2: 0.378

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.7→49.54 Å / Cor.coef. Fo:Fc: 0.873 / Cor.coef. Fo:Fc free: 0.833 / SU B: 87.415 / SU ML: 1.09 / Cross valid method: THROUGHOUT / ESU R Free: 0.874 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.30787 1906 5 %RANDOM
Rwork0.27879 ---
obs0.28029 35841 97.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.426 Å2
Baniso -1Baniso -2Baniso -3
1--3.68 Å2-0 Å20.25 Å2
2--13.04 Å2-0 Å2
3----9.35 Å2
Refinement stepCycle: 1 / Resolution: 3.7→49.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19920 0 104 18 20042
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01220478
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1551.63427722
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.88352484
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.36522.9271107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.886153546
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.19715117
X-RAY DIFFRACTIONr_chiral_restr0.0880.22622
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215734
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)
11A286670.06
12B286670.06
21A281510.09
22C281510.09
31B283440.08
32C283440.08
LS refinement shellResolution: 3.7→3.796 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.439 148 -
Rwork0.392 2686 -
obs--99.13 %

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