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- PDB-9ukr: Crystal structure of glycogen phosphorylase from E. coli in compl... -

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Basic information

Entry
Database: PDB / ID: 9ukr
TitleCrystal structure of glycogen phosphorylase from E. coli in complex with AMP
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
ADENOSINE MONOPHOSPHATE / Glycogen phosphorylase
Similarity search - Component
Biological speciesEscherichia coli K12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.55 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: Takai, M. / Shobu, K. / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)564,96414
Polymers562,1866
Non-polymers2,7788
Water00
1
A: Glycogen phosphorylase
B: Glycogen phosphorylase
C: Glycogen phosphorylase
D: Glycogen phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)376,87410
Polymers374,7914
Non-polymers2,0836
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Glycogen phosphorylase
F: Glycogen phosphorylase
hetero molecules

E: Glycogen phosphorylase
F: Glycogen phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)376,1808
Polymers374,7914
Non-polymers1,3894
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_456-x-1,y,-z+11
Unit cell
Length a, b, c (Å)134.915, 204.539, 263.337
Angle α, β, γ (deg.)90.000, 104.566, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y

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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 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: P0AC86, glycogen phosphorylase
#2: Chemical
ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
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: 3.13 Å3/Da / Density % sol: 60.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: Protein conc: 10.4mg/mL; Reservoir: 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: Jan 28, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.55→47.46 Å / Num. obs: 83087 / % possible obs: 99.7 % / Redundancy: 3.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.06 / Rrim(I) all: 0.114 / Net I/σ(I): 7.1
Reflection shellResolution: 3.55→3.62 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.861 / Num. unique obs: 4574 / CC1/2: 0.516 / Rpim(I) all: 0.561 / Rrim(I) all: 1.031 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.55→42.79 Å / SU ML: 0.5719 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.8078
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2722 4253 5.12 %
Rwork0.2235 78804 -
obs0.226 83057 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 121.04 Å2
Refinement stepCycle: LAST / Resolution: 3.55→42.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms39006 0 184 0 39190
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003140086
X-RAY DIFFRACTIONf_angle_d0.67554410
X-RAY DIFFRACTIONf_chiral_restr0.04315910
X-RAY DIFFRACTIONf_plane_restr0.00477044
X-RAY DIFFRACTIONf_dihedral_angle_d16.85214764
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.55-3.590.35861360.33172661X-RAY DIFFRACTION99.96
3.59-3.630.39541250.32822615X-RAY DIFFRACTION99.85
3.63-3.680.38291520.31942584X-RAY DIFFRACTION99.85
3.68-3.720.38771550.31542660X-RAY DIFFRACTION99.86
3.72-3.770.36821550.31722568X-RAY DIFFRACTION99.96
3.77-3.820.37571560.30452648X-RAY DIFFRACTION99.89
3.82-3.880.34951450.31062596X-RAY DIFFRACTION99.93
3.88-3.940.31631540.29112636X-RAY DIFFRACTION99.93
3.94-40.33061340.28332607X-RAY DIFFRACTION99.89
4-4.060.30931350.27332645X-RAY DIFFRACTION99.86
4.06-4.130.29631360.27242611X-RAY DIFFRACTION99.96
4.13-4.210.32061480.26282636X-RAY DIFFRACTION100
4.21-4.290.3181660.26062580X-RAY DIFFRACTION99.78
4.29-4.380.2891330.25942675X-RAY DIFFRACTION99.89
4.38-4.470.33011600.2582574X-RAY DIFFRACTION100
4.47-4.580.29551460.23992642X-RAY DIFFRACTION99.79
4.58-4.690.28271450.24482624X-RAY DIFFRACTION99.89
4.69-4.820.2511480.23982612X-RAY DIFFRACTION99.86
4.82-4.960.25931380.22472624X-RAY DIFFRACTION99.93
4.96-5.120.26151330.22782672X-RAY DIFFRACTION99.86
5.12-5.30.28151170.22722644X-RAY DIFFRACTION99.71
5.3-5.510.27241460.22882608X-RAY DIFFRACTION99.82
5.51-5.760.27881340.22662643X-RAY DIFFRACTION99.86
5.76-6.070.26361400.23292635X-RAY DIFFRACTION99.82
6.07-6.440.2731090.24362691X-RAY DIFFRACTION99.68
6.44-6.940.27221350.22752622X-RAY DIFFRACTION99.71
6.94-7.630.26951630.20222643X-RAY DIFFRACTION99.75
7.64-8.730.21251710.16722609X-RAY DIFFRACTION99.11
8.73-10.970.17711290.12292624X-RAY DIFFRACTION98.74
10.97-42.790.18611090.1462615X-RAY DIFFRACTION95.41

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