[English] 日本語
Yorodumi
- EMDB-17409: Cyanide dihydratase from Bacillus pumilus C1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-17409
TitleCyanide dihydratase from Bacillus pumilus C1
Map dataCyanide dihydratase from Bacillus pumilus C1
Sample
  • Complex: Wildtype cyanide dihydratase from Bacillus pumilus C1
    • Protein or peptide: Cyanide dihydratase
KeywordsCyanide degrading enzyme / HYDROLASE
Function / homology
Function and homology information


nitrilase activity / detoxification of nitrogen compound / nitrile hydratase activity
Similarity search - Function
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 speciesBacillus pumilus (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 3.83 Å
AuthorsMulelu AE / Reitz J / van Rooyen JM / Scheffer M / Frangakis AS / Dlamini LS / Woodward JD / Benedik MJ / Sewell BT
Funding support South Africa, 1 items
OrganizationGrant numberCountry
National Research Foundation in South Africa South Africa
CitationJournal: To Be Published
Title: The Role of Histidine Residues in the Oligomerization of Cyanide Dihydratase from Bacillus pumilus C1
Authors: Mulelu AE / Reitz J / van Rooyen J / Scheffer M / Frangakis AS / Dlamini LS / Woodward JD / Benedik MJ / Sewell BT
History
DepositionMay 22, 2023-
Header (metadata) releaseAug 16, 2023-
Map releaseAug 16, 2023-
UpdateAug 16, 2023-
Current statusAug 16, 2023Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_17409.png

Downloads & links

-
Map

FileDownload / File: emd_17409.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCyanide dihydratase from Bacillus pumilus C1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 300 pix.
= 315. Å		1.05 Å/pix.
x 300 pix.
= 315. Å		1.05 Å/pix.
x 300 pix.
= 315. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0119
Minimum - Maximum-0.020919774 - 0.04766187
Average (Standard dev.)0.0003063033 (±0.0022641555)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 315.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : Wildtype cyanide dihydratase from Bacillus pumilus C1

EntireName: Wildtype cyanide dihydratase from Bacillus pumilus C1
Components
  • Complex: Wildtype cyanide dihydratase from Bacillus pumilus C1
    • Protein or peptide: Cyanide dihydratase

-
Supramolecule #1: Wildtype cyanide dihydratase from Bacillus pumilus C1

SupramoleculeName: Wildtype cyanide dihydratase from Bacillus pumilus C1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Homo-oligomeric 18mer expressed recombinantly without a purification tag.
Source (natural)Organism: Bacillus pumilus (bacteria)
Molecular weightTheoretical: 0.666 kDa/nm

-
Macromolecule #1: Cyanide dihydratase

MacromoleculeName: Cyanide dihydratase / type: protein_or_peptide / ID: 1 / Number of copies: 17 / Enantiomer: LEVO
Source (natural)Organism: Bacillus pumilus (bacteria)
Molecular weightTheoretical: 35.941418 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SIYPKFRAAA VQAAPIYLNL EASVEKSCEL IDEAASNGAK LVAFPEAFLP GYPWFAFIGH PEYTRKFYHE LYKNAVEIPS LAIQKISEA AKRNETYVCI SCSEKDGGSL YLAQLWFNPN GDLIGKHRKM RASVAERLIW GDGSGSMMPV FQTEIGNLGG L MCWEHQVP ...String:
SIYPKFRAAA VQAAPIYLNL EASVEKSCEL IDEAASNGAK LVAFPEAFLP GYPWFAFIGH PEYTRKFYHE LYKNAVEIPS LAIQKISEA AKRNETYVCI SCSEKDGGSL YLAQLWFNPN GDLIGKHRKM RASVAERLIW GDGSGSMMPV FQTEIGNLGG L MCWEHQVP LDLMAMNAQN EQVHVASWPG YFDDEISSRY YAIATQTFVL MTSSIYTEEM KEMICLTQEQ RDYFETFKSG HT CIYGPDG EPISDMVPAE TEGIAYAEID VERVIDYKYY IDPAGHYSNQ SLSMNFNQQP TPVVKHLNHQ KNEVFTYEDI

UniProtKB: Cyanide dihydratase

-
Experimental details

-
Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

-
Sample preparation

Concentration0.2 mg/mL
BufferpH: 5.4 / Component - Concentration: 50.0 mM / Component - Formula: C6H8O7 / Component - Name: citrate
GridModel: Quantifoil R2/2 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK I

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 59.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 16.9 Å
Applied symmetry - Helical parameters - Δ&Phi: -77 °
Applied symmetry - Helical parameters - Axial symmetry: C2 (2 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 3.83 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 120943
Startup modelType of model: INSILICO MODEL
Final angle assignmentType: NOT APPLICABLE

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-8p4i:
Cyanide dihydratase from Bacillus pumilus C1

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more