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- EMDB-68637: Oligomer Nitrilase M24 -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-68637
TitleOligomer Nitrilase M24
Map data
Sample
  • Complex: Oligomer Nitrilase
    • Protein or peptide: Nitrilase
KeywordsOligomer Nitrilase M24 / HYDROLASE
Function / homology
Function and homology information


nitrilase / nitrilase activity
Similarity search - Function
Nitrilases / cyanide hydratase active site signature. / Nitrilase/Cyanide hydratase / Nitrilases / cyanide hydratase signature 1. / Nitrilase/cyanide hydratase, conserved site / Carbon-nitrogen hydrolase domain profile. / Carbon-nitrogen hydrolase superfamily / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase
Similarity search - Domain/homology
Biological speciesAcidovorax facilis (bacteria)
Methodhelical reconstruction / negative staining / Resolution: 20.0 Å
AuthorsXue YP
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Structure of Nitrilase M24
Authors: Xue YP
History
DepositionJan 21, 2026-
Header (metadata) releaseJul 29, 2026-
Map releaseJul 29, 2026-
UpdateJul 29, 2026-
Current statusJul 29, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_68637.png

Downloads & links

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Map

FileDownload / File: emd_68637.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.66 Å/pix.
x 200 pix.
= 532. Å		2.66 Å/pix.
x 200 pix.
= 532. Å		2.66 Å/pix.
x 200 pix.
= 532. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.66 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.65
Minimum - Maximum-1.2386867 - 3.7327392
Average (Standard dev.)-0.016107542 (±0.49079317)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 532.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_68637_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_68637_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Oligomer Nitrilase

EntireName: Oligomer Nitrilase
Components
  • Complex: Oligomer Nitrilase
    • Protein or peptide: Nitrilase

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Supramolecule #1: Oligomer Nitrilase

SupramoleculeName: Oligomer Nitrilase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Acidovorax facilis (bacteria)

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Macromolecule #1: Nitrilase

MacromoleculeName: Nitrilase / type: protein_or_peptide / ID: 1 / Number of copies: 32 / Enantiomer: LEVO / EC number: nitrilase
Source (natural)Organism: Acidovorax facilis (bacteria)
Molecular weightTheoretical: 38.146023 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MVSYNSKFLA ATVQAEPVWL DADATIDKSI GIIEEAAQKG ASLIAFPEVF IPGYPYWAWL GDVKYSLSFT SRYHENSLEL GDDRMRRLQ LAARRNKIAL VMGYSEREAG SRYLSQVFID ERGEIVANRR KLKPTHVERT IYGEGNGTDF LTHDFAFGRV G GLNCWEHV ...String:
MVSYNSKFLA ATVQAEPVWL DADATIDKSI GIIEEAAQKG ASLIAFPEVF IPGYPYWAWL GDVKYSLSFT SRYHENSLEL GDDRMRRLQ LAARRNKIAL VMGYSEREAG SRYLSQVFID ERGEIVANRR KLKPTHVERT IYGEGNGTDF LTHDFAFGRV G GLNCWEHV QPLSKFMMYS LGEQVHVASW PAMSPLQPDV FQMSIEANAT VTRSYAIEGQ TFVLCSTQVI GPSAIETFCL ND EQRALLP QGCGWARIYG PDGSELAKPL AEDAEGILYA EIDLEQILLA KAGADPVGHY SRPDVLSLQY DPRNHTPVHR IGI DGRLDV NTRSRVENFR LRQAA

UniProtKB: Nitrilase

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Experimental details

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Structure determination

Methodnegative staining
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

BufferpH: 7
StainingType: NEGATIVE / Material: Uranyl Acetate

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Electron microscopy

MicroscopeTFS TALOS
Image recordingFilm or detector model: FEI CETA (4k x 4k) / Average electron dose: 20.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 17.67 Å
Applied symmetry - Helical parameters - Δ&Phi: -72.11 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 4552
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final angle assignmentType: NOT APPLICABLE

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