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- PDB-22rx: Oligomer Nitrilase ACN -

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Basic information

Entry
Database: PDB / ID: 22rx
TitleOligomer Nitrilase ACN
ComponentsRegioselective nitrilase
KeywordsHYDROLASE / Oligomer Nitrilase ACN
Function / homology:
Function and homology information
Biological speciesAcidovorax facilis (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / negative staining / Resolution: 17 Å
AuthorsXue, Y.P. / Xue, Y.P.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Structure of Oligomer Nitrilase ACN
Authors: Xue, Y.P.
History
DepositionJan 21, 2026Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 29, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Regioselective nitrilase
B: Regioselective nitrilase
C: Regioselective nitrilase
D: Regioselective nitrilase
E: Regioselective nitrilase
F: Regioselective nitrilase
G: Regioselective nitrilase
H: Regioselective nitrilase
I: Regioselective nitrilase
J: Regioselective nitrilase
K: Regioselective nitrilase
L: Regioselective nitrilase
M: Regioselective nitrilase
N: Regioselective nitrilase
O: Regioselective nitrilase
P: Regioselective nitrilase
Q: Regioselective nitrilase
R: Regioselective nitrilase
S: Regioselective nitrilase
T: Regioselective nitrilase
U: Regioselective nitrilase
V: Regioselective nitrilase
W: Regioselective nitrilase
X: Regioselective nitrilase
Y: Regioselective nitrilase
Z: Regioselective nitrilase
a: Regioselective nitrilase
b: Regioselective nitrilase
c: Regioselective nitrilase
d: Regioselective nitrilase
e: Regioselective nitrilase
f: Regioselective nitrilase
g: Regioselective nitrilase
h: Regioselective nitrilase
i: Regioselective nitrilase
j: Regioselective nitrilase
k: Regioselective nitrilase
l: Regioselective nitrilase
m: Regioselective nitrilase
n: Regioselective nitrilase


Theoretical massNumber of molelcules
Total (without water)1,525,35840
Polymers1,525,35840
Non-polymers00
Water00
1


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

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Components

#1: Protein ...
Regioselective nitrilase


Mass: 38133.949 Da / Num. of mol.: 40
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acidovorax facilis (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0U1TDG4, nitrilase
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Oligomer Nitrilase / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Acidovorax facilis (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: YES / Vitrification applied: NO
EM stainingType: NEGATIVE / Material: Uranyl Acetate

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: TFS TALOS F200C
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 20 e/Å2 / Film or detector model: FEI CETA (4k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -74.72 ° / Axial rise/subunit: 17.42 Å / Axial symmetry: C1
3D reconstructionResolution: 17 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 90423 / Symmetry type: HELICAL

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