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- PDB-9qqk: GH161 phosphorylase in complex with beta-1,3 glucooligosaccharide -

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Basic information

Entry
Database: PDB / ID: 9qqk
TitleGH161 phosphorylase in complex with beta-1,3 glucooligosaccharide
Componentsgh161 phosphorylase
KeywordsCYTOSOLIC PROTEIN / phosphorylase / gh161 / laminarin
Biological speciesgut metagenome (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.14 Å
AuthorsCooper, N. / Cioci, G. / Ladeveze, S. / Potocki-Veronese, G. / Moulis, C. / Remaud-Simeon, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acs Catalysis / Year: 2025
Title: Structural and Functional Dissection of GH161 beta-Glucan Phosphorylases: Molecular Specificities and Dynamics of Catalysis of Dimeric GH-Q Enzymes
Authors: Cooper, N.J. / Ladeveze, S. / Li, A. / Shayan, R. / Faure, R. / Ropartz, D. / Terrapon, N. / Lombard, V. / Henrissat, B. / Remaud-Simeon, M. / Potocki-Veronese, G. / Moulis, C. / Cioci, G.
History
DepositionApr 1, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 10, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: gh161 phosphorylase
B: gh161 phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)241,3934
Polymers239,7362
Non-polymers1,6572
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "B"
d_2ens_1chain "A"

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11GLUGLUHISHISBB6 - 10436 - 1043
d_12BGCBGCBGCBGCDD1
d_13BGCBGCBGCBGCDD2
d_14BGCBGCBGCBGCDD3
d_15BGCBGCBGCBGCDD4
d_16BGCBGCBGCBGCDD5
d_21GLUGLUHISHISAA6 - 10436 - 1043
d_22BGCBGCBGCBGCCC1
d_23BGCBGCBGCBGCCC2
d_24BGCBGCBGCBGCCC3
d_25BGCBGCBGCBGCCC4
d_26BGCBGCBGCBGCCC5

NCS oper: (Code: givenMatrix: (-0.999995284948, -0.00267086007824, -0.00151545011897), (0.00267036785125, -0.999996381183, 0.000326736294747), (-0.00151631730176, 0.000322687944891, 0.999998798326) ...NCS oper: (Code: given
Matrix: (-0.999995284948, -0.00267086007824, -0.00151545011897), (0.00267036785125, -0.999996381183, 0.000326736294747), (-0.00151631730176, 0.000322687944891, 0.999998798326)
Vector: 288.498482622, 287.503771104, 0.208708837364)

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Components

#1: Protein gh161 phosphorylase


Mass: 119868.008 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) gut metagenome (others) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Polysaccharide beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D- ...beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 828.719 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-3DGlcpb1-3DGlcpb1-3DGlcpb1-3DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,5,4/[a2122h-1b_1-5]/1-1-1-1-1/a3-b1_b3-c1_c3-d1_d3-e1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(3+1)][b-D-Glcp]{[(3+1)][b-D-Glcp]{[(3+1)][b-D-Glcp]{[(3+1)][b-D-Glcp]{}}}}}LINUCSPDB-CARE
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: gh161 phosphorylase / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.12 MDa / Experimental value: NO
Source (natural)Organism: uncultured bacterium (environmental samples)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil R1.2/1.3
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 4 K

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 150000 X / Nominal defocus max: 2800 nm / Nominal defocus min: 1800 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Image recordingAverage exposure time: 5 sec. / Electron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 5242

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Processing

EM software
IDNameVersionCategory
1RELION4particle selection
4RELION4CTF correction
7UCSF Chimeramodel fitting
9PHENIX1.21.2_5419model refinement
10RELION4initial Euler assignment
11cryoSPARCfinal Euler assignment
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 81913
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.14 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 22729 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingPDB-ID: 9H2R

9h2r
PDB Unreleased entry


Accession code: 9H2R / Source name: PDB / Type: experimental model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 140.39 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.001517152
ELECTRON MICROSCOPYf_angle_d0.379423172
ELECTRON MICROSCOPYf_chiral_restr0.03832472
ELECTRON MICROSCOPYf_plane_restr0.00283008
ELECTRON MICROSCOPYf_dihedral_angle_d9.32966546
Refine LS restraints NCSType: NCS constraints / Rms dev position: 2.9543324822E-12 Å

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