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- PDB-9v16: Crystal structure of E. coli glycogen phosphorylase N185A/R267E m... -

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Basic information

Entry
Database: PDB / ID: 9v16
TitleCrystal structure of E. coli glycogen phosphorylase N185A/R267E mutant 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 K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.45 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
DepositionMay 19, 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

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Assembly

Deposited unit
A: Glycogen phosphorylase
B: Glycogen phosphorylase
C: Glycogen phosphorylase
D: Glycogen phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)375,8958
Polymers374,5064
Non-polymers1,3894
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11510 Å2
ΔGint-24 kcal/mol
Surface area113290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)185.604, 185.604, 451.242
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein
Glycogen phosphorylase


Mass: 93626.562 Da / Num. of mol.: 4 / Mutation: N185A/R267E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: glgP, glgY, b3428, JW3391 / Plasmid: pET28-a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0AC86, glycogen phosphorylase
#2: Chemical
ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 4 / 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: 5.19 Å3/Da / Density % sol: 76.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 2% v/v 1,4-dioxane, 0.1M Tris pH 8.0, 15% w/v polyethylene glycol 3350 (The crystal was soaked in a solution supplemented with 40 mM AMP before data collection)

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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: Apr 23, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.45→49.5 Å / Num. obs: 98722 / % possible obs: 95.3 % / Redundancy: 9.6 % / Biso Wilson estimate: 111.35 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.164 / Rpim(I) all: 0.054 / Rrim(I) all: 0.173 / Net I/σ(I): 12
Reflection shellResolution: 3.45→3.51 Å / Redundancy: 10 % / Rmerge(I) obs: 2 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4913 / CC1/2: 0.81 / Rpim(I) all: 0.652 / Rrim(I) all: 2.11 / % possible all: 96.7

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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: 3.45→49.45 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2351 4971 5.04 %
Rwork0.1921 --
obs0.1942 98610 94.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.45→49.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25677 0 92 0 25769
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01126349
X-RAY DIFFRACTIONf_angle_d1.40835758
X-RAY DIFFRACTIONf_dihedral_angle_d17.669708
X-RAY DIFFRACTIONf_chiral_restr0.0713901
X-RAY DIFFRACTIONf_plane_restr0.0144623
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.45-3.490.42831710.35613106X-RAY DIFFRACTION96
3.49-3.530.4621620.33953123X-RAY DIFFRACTION96
3.53-3.570.31481630.3173131X-RAY DIFFRACTION96
3.57-3.620.39811690.3063103X-RAY DIFFRACTION96
3.62-3.670.31871650.28973109X-RAY DIFFRACTION96
3.67-3.720.33681610.28943149X-RAY DIFFRACTION96
3.72-3.770.35041580.26893098X-RAY DIFFRACTION96
3.77-3.830.29081530.25913125X-RAY DIFFRACTION96
3.83-3.890.26761590.2473142X-RAY DIFFRACTION96
3.89-3.950.23971700.23043128X-RAY DIFFRACTION96
3.95-4.020.2721880.2293079X-RAY DIFFRACTION96
4.02-4.090.29781700.2333105X-RAY DIFFRACTION95
4.09-4.170.30011770.23013134X-RAY DIFFRACTION95
4.17-4.250.24651760.22013087X-RAY DIFFRACTION95
4.25-4.350.25141570.20223119X-RAY DIFFRACTION95
4.35-4.450.26481850.19513108X-RAY DIFFRACTION95
4.45-4.560.24291530.19133118X-RAY DIFFRACTION95
4.56-4.680.19381590.1872972X-RAY DIFFRACTION91
4.68-4.820.19591460.17053070X-RAY DIFFRACTION93
4.82-4.970.24791840.17663119X-RAY DIFFRACTION95
4.98-5.150.19931610.16063145X-RAY DIFFRACTION95
5.15-5.360.20391740.17013089X-RAY DIFFRACTION94
5.36-5.60.20931610.17483155X-RAY DIFFRACTION95
5.6-5.90.20461750.17083090X-RAY DIFFRACTION94
5.9-6.270.20661740.18293147X-RAY DIFFRACTION94
6.27-6.750.21851630.16793135X-RAY DIFFRACTION94
6.75-7.420.20481490.17343181X-RAY DIFFRACTION94
7.43-8.490.18521560.13553167X-RAY DIFFRACTION93
8.5-10.680.15081560.12343134X-RAY DIFFRACTION91
10.69-49.450.22631760.17693271X-RAY DIFFRACTION90

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