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- PDB-9ukq: Crystal structure of glycogen phosphorylase from Escherichia coli -

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Basic information

Entry
Database: PDB / ID: 9ukq
TitleCrystal structure of glycogen phosphorylase from Escherichia coli
ComponentsGlycogen phosphorylase
KeywordsTRANSFERASE / glycogen phosphorylase
Function / homology
Function and homology information


glycogen phosphorylase / glycogen phosphorylase activity / glycogen catabolic process / pyridoxal phosphate binding / protein homodimerization activity / cytoplasm
Similarity search - Function
Glycogen/starch/alpha-glucan phosphorylase / Phosphorylase pyridoxal-phosphate attachment site / Phosphorylase pyridoxal-phosphate attachment site. / Glycosyl transferase, family 35 / Carbohydrate phosphorylase
Similarity search - Domain/homology
Glycogen phosphorylase
Similarity search - Component
Biological speciesEscherichia coli K12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsTakai, M. / Shobu, K. / Fukuda, Y. / Inoue, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: To Be Published
Title: Structural and mechanistic diversity of glycogen phosphorylases from gut bacteria
Authors: Shobu, K. / Takai, M. / Tanino, H. / Fukuda, Y. / Inoue, T.
History
DepositionApr 18, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 18, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycogen phosphorylase
B: Glycogen phosphorylase
C: Glycogen phosphorylase
D: Glycogen phosphorylase
E: Glycogen phosphorylase
F: Glycogen phosphorylase


Theoretical massNumber of molelcules
Total (without water)562,1866
Polymers562,1866
Non-polymers00
Water00
1
A: Glycogen phosphorylase
B: Glycogen phosphorylase
C: Glycogen phosphorylase
D: Glycogen phosphorylase


Theoretical massNumber of molelcules
Total (without water)374,7914
Polymers374,7914
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Glycogen phosphorylase
F: Glycogen phosphorylase

E: Glycogen phosphorylase
F: Glycogen phosphorylase


Theoretical massNumber of molelcules
Total (without water)374,7914
Polymers374,7914
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Unit cell
Length a, b, c (Å)134.769, 205.603, 264.075
Angle α, β, γ (deg.)90.00, 104.35, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Glycogen phosphorylase


Mass: 93697.672 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K12 (bacteria) / Gene: glgP, glgY, b3428, JW3391 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AC86, glycogen phosphorylase
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: 3.15 Å3/Da / Density % sol: 60.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: Protein conc: 10.4mg/mL; 0.1M MES pH 6.0, 9% (v/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 27, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.5→47.69 Å / Num. obs: 86898 / % possible obs: 99.1 % / Redundancy: 3.5 % / CC1/2: 0.994 / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.083 / Rrim(I) all: 0.157 / Net I/σ(I): 6.2
Reflection shellResolution: 3.5→3.56 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.949 / Num. unique obs: 4462 / CC1/2: 0.596 / Rpim(I) all: 0.576 / Rrim(I) all: 1.112 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→46.21 Å / SU ML: 0.53 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2731 4436 5.11 %
Rwork0.2307 --
obs0.2329 86855 99.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.5→46.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms38963 0 0 0 38963
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00339842
X-RAY DIFFRACTIONf_angle_d0.66554047
X-RAY DIFFRACTIONf_dihedral_angle_d5.1195359
X-RAY DIFFRACTIONf_chiral_restr0.0455872
X-RAY DIFFRACTIONf_plane_restr0.0057028
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.540.37491600.35862781X-RAY DIFFRACTION100
3.54-3.580.34841590.33632717X-RAY DIFFRACTION100
3.58-3.630.34731480.31892794X-RAY DIFFRACTION100
3.63-3.670.37021470.31482727X-RAY DIFFRACTION100
3.67-3.720.33261440.31232802X-RAY DIFFRACTION100
3.72-3.770.34991430.31042718X-RAY DIFFRACTION100
3.77-3.820.38871550.31112752X-RAY DIFFRACTION100
3.82-3.880.34021370.2922760X-RAY DIFFRACTION100
3.88-3.940.33021440.28992790X-RAY DIFFRACTION100
3.94-4.010.32111340.27752743X-RAY DIFFRACTION100
4.01-4.080.32651620.27892773X-RAY DIFFRACTION100
4.08-4.150.30141640.26162704X-RAY DIFFRACTION100
4.15-4.230.28671540.26672774X-RAY DIFFRACTION100
4.23-4.320.26611330.25662745X-RAY DIFFRACTION100
4.32-4.410.31751760.24862751X-RAY DIFFRACTION99
4.41-4.510.31681430.2492767X-RAY DIFFRACTION100
4.51-4.620.25921470.23322730X-RAY DIFFRACTION100
4.62-4.750.29171630.23442754X-RAY DIFFRACTION99
4.75-4.890.26351400.2322770X-RAY DIFFRACTION99
4.89-5.050.23441250.22042754X-RAY DIFFRACTION99
5.05-5.230.25911340.22362745X-RAY DIFFRACTION99
5.23-5.440.25631380.22552764X-RAY DIFFRACTION99
5.44-5.680.31151440.23082785X-RAY DIFFRACTION99
5.68-5.980.2921540.23472743X-RAY DIFFRACTION99
5.98-6.350.28311330.24322745X-RAY DIFFRACTION99
6.36-6.840.30021390.23322756X-RAY DIFFRACTION98
6.84-7.530.25761840.20762665X-RAY DIFFRACTION98
7.53-8.610.20861580.17262719X-RAY DIFFRACTION98
8.62-10.830.1481230.13382741X-RAY DIFFRACTION97
10.83-46.210.19681510.14922650X-RAY DIFFRACTION93

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