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- PDB-9dgh: Focused region on azoRhuA-bCDRhuA co-assembled nanotubes -

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Basic information

Entry
Database: PDB / ID: 9dgh
TitleFocused region on azoRhuA-bCDRhuA co-assembled nanotubes
ComponentsRhamnulose-1-phosphate aldolase
KeywordsLYASE / Assembly
Function / homology
Function and homology information


rhamnulose-1-phosphate aldolase / rhamnulose-1-phosphate aldolase activity / rhamnose catabolic process / pentose catabolic process / aldehyde-lyase activity / metal ion binding / identical protein binding / cytosol
Similarity search - Function
Rhamnulose-1-phosphate aldolase / : / Class II aldolase/adducin N-terminal / Class II Aldolase and Adducin N-terminal domain / Class II Aldolase and Adducin N-terminal domain / Class II aldolase/adducin N-terminal domain superfamily
Similarity search - Domain/homology
: / Rhamnulose-1-phosphate aldolase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.03 Å
AuthorsZhang, Z. / Sonani, R.R. / Wang, F. / Egelman, E.H. / Tezcan, F.A.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States) United States
CitationJournal: Chem / Year: 2025
Title: Design of light-and chemically responsive protein assemblies through host-guest interactions
Authors: Zhang, Z. / Chiang, H.T. / Xia, Y. / Avakyan, N. / Sonani, R.R. / Wang, F. / Egelman, E.H. / De Yoreo, J.J. / Pozzo, L.D. / Tezcan, F.A.
History
DepositionSep 2, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Rhamnulose-1-phosphate aldolase
D: Rhamnulose-1-phosphate aldolase
B: Rhamnulose-1-phosphate aldolase
C: Rhamnulose-1-phosphate aldolase
E: Rhamnulose-1-phosphate aldolase
H: Rhamnulose-1-phosphate aldolase
F: Rhamnulose-1-phosphate aldolase
G: Rhamnulose-1-phosphate aldolase
I: Rhamnulose-1-phosphate aldolase
L: Rhamnulose-1-phosphate aldolase
J: Rhamnulose-1-phosphate aldolase
K: Rhamnulose-1-phosphate aldolase
M: Rhamnulose-1-phosphate aldolase
P: Rhamnulose-1-phosphate aldolase
N: Rhamnulose-1-phosphate aldolase
O: Rhamnulose-1-phosphate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)485,38536
Polymers481,41416
Non-polymers3,97120
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Rhamnulose-1-phosphate aldolase


Mass: 30088.361 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rhaD, rhuA, b3902, JW3873 / Production host: Escherichia coli (E. coli)
References: UniProt: P32169, rhamnulose-1-phosphate aldolase
#2: Polysaccharide Cyclic alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranuronic acid-(1-4)- ...Cyclic alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranuronic acid-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranuronic acid-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 1180.967 Da / Num. of mol.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
WURCS=2.0/2,7,7/[a2122h-1a_1-5][a2122A-1a_1-5]/1-1-1-2-1-1-2/a1-g4_a4-b1_b4-c1_c4-d1_d4-e1_e4-f1_f4-g1WURCSPDB2Glycan 1.1.0
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-A1A4G / 1-[4-(2-phenylhydrazin-1-yl)phenyl]pyrrolidine-2,5-dione


Mass: 281.309 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H15N3O2
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Helical assembly of azobenzene and beta-cyclodextrin modified RhuA
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2100 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
4cryoSPARCCTF correction
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.03 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 440307 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 66.61 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003834970
ELECTRON MICROSCOPYf_angle_d0.586247682
ELECTRON MICROSCOPYf_chiral_restr0.04115414
ELECTRON MICROSCOPYf_plane_restr0.00436104
ELECTRON MICROSCOPYf_dihedral_angle_d17.173812776

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