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- PDB-9maq: Glycogen phosphorylase from D. longicatena -

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Basic information

Entry
Database: PDB / ID: 9maq
TitleGlycogen phosphorylase from D. longicatena
ComponentsAlpha-1,4 glucan phosphorylase
KeywordsSTRUCTURAL PROTEIN / glycogen metabolism / cryo-EM / gut bacteria
Function / homology
Function and homology information


glycogen phosphorylase / glycogen phosphorylase activity / glycogen catabolic process / pyridoxal phosphate binding / 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
Alpha-1,4 glucan phosphorylase
Similarity search - Component
Biological speciesDorea longicatena DSM 13814 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å
AuthorsTakai, M. / 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 phosphrylases from gut bacteria
Authors: Shobu, K. / Takai, M. / Fukuda, Y. / Inoue, T.
History
DepositionMar 14, 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: Alpha-1,4 glucan phosphorylase
B: Alpha-1,4 glucan phosphorylase


Theoretical massNumber of molelcules
Total (without water)172,4762
Polymers172,4762
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-15 kcal/mol
Surface area53150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.969, 122.851, 136.004
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Alpha-1,4 glucan phosphorylase


Mass: 86238.117 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dorea longicatena DSM 13814 (bacteria) / Gene: glgP, malP_2, ERS852423_02459, GT528_00800 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A174FL20, 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: 2.52 Å3/Da / Density % sol: 51.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.2 M Potassium thiocyanate, 28 % 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: 3.8→49.29 Å / Num. obs: 17775 / % possible obs: 99.9 % / Redundancy: 6.7 % / CC1/2: 0.993 / Rmerge(I) obs: 0.249 / Rpim(I) all: 0.104 / Rrim(I) all: 0.27 / Net I/σ(I): 10.1
Reflection shellResolution: 3.8→4.25 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.635 / Mean I/σ(I) obs: 5 / Num. unique obs: 4958 / CC1/2: 0.939 / Rpim(I) all: 0.262 / Rrim(I) all: 0.687 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
REFMAC5.5refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.8→48.56 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2655 859 4.85 %
Rwork0.2014 --
obs0.2046 17716 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.8→48.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12128 0 0 0 12128
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00412366
X-RAY DIFFRACTIONf_angle_d0.67816728
X-RAY DIFFRACTIONf_dihedral_angle_d7.0471638
X-RAY DIFFRACTIONf_chiral_restr0.0441856
X-RAY DIFFRACTIONf_plane_restr0.0052148
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.8-4.040.34221190.26312761X-RAY DIFFRACTION100
4.04-4.350.28751440.23052769X-RAY DIFFRACTION100
4.35-4.790.29321340.20672789X-RAY DIFFRACTION100
4.79-5.480.27641410.19292789X-RAY DIFFRACTION100
5.48-6.90.24621680.21692801X-RAY DIFFRACTION100
6.9-48.560.22421530.16012948X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 26.8738 Å / Origin y: -62.6178 Å / Origin z: 36.1385 Å
111213212223313233
T0.6357 Å20.0742 Å20.0114 Å2-0.8002 Å2-0.046 Å2--0.7055 Å2
L0.4414 °2-0.5914 °20.3223 °2-1.5988 °2-0.6496 °2--0.6084 °2
S-0.165 Å °-0.1872 Å °0.0398 Å °0.4037 Å °0.1989 Å °0.0658 Å °-0.0914 Å °-0.2994 Å °-0.0204 Å °
Refinement TLS groupSelection details: all

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