[English] 日本語
Yorodumi
- PDB-8p4i: Cyanide dihydratase from Bacillus pumilus C1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8p4i
TitleCyanide dihydratase from Bacillus pumilus C1
ComponentsCyanide dihydratase
KeywordsHYDROLASE / Cyanide degrading enzyme
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 superfamily / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase domain profile. / Carbon-nitrogen hydrolase
Similarity search - Domain/homology
Biological speciesBacillus pumilus (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.83 Å
AuthorsMulelu, A.E. / Reitz, J. / van Rooyen, J.M. / Scheffer, M. / Frangakis, A.S. / Dlamini, L.S. / Woodward, J.D. / Benedik, M.J. / Sewell, B.T.
Funding support South Africa, 1items
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, A.E. / Reitz, J. / van Rooyen, J. / Scheffer, M. / Frangakis, A.S. / Dlamini, L.S. / Woodward, J.D. / Benedik, M.J. / Sewell, B.T.
History
DepositionMay 22, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 16, 2023Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Cyanide dihydratase
D: Cyanide dihydratase
F: Cyanide dihydratase
G: Cyanide dihydratase
H: Cyanide dihydratase
I: Cyanide dihydratase
J: Cyanide dihydratase
K: Cyanide dihydratase
L: Cyanide dihydratase
M: Cyanide dihydratase
N: Cyanide dihydratase
O: Cyanide dihydratase
P: Cyanide dihydratase
Q: Cyanide dihydratase
R: Cyanide dihydratase
S: Cyanide dihydratase
U: Cyanide dihydratase


Theoretical massNumber of molelcules
Total (without water)611,00417
Polymers611,00417
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area79630 Å2
ΔGint-438 kcal/mol
Surface area205790 Å2

-
Components

#1: Protein
Cyanide dihydratase


Mass: 35941.418 Da / Num. of mol.: 17
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus pumilus (bacteria) / Gene: cynD / Production host: Escherichia coli (E. coli) / References: UniProt: Q8GGL4

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Wildtype cyanide dihydratase from Bacillus pumilus C1 / Type: COMPLEX
Details: Homo-oligomeric 18mer expressed recombinantly without a purification tag.
Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.666 kDa/nm / Experimental value: YES
Source (natural)Organism: Bacillus pumilus (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 5.4
Buffer componentConc.: 50 mM / Name: citrate / Formula: C6H8O7
SpecimenConc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: OTHER / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 59.4 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

-
Processing

EM software
IDNameVersionCategoryDetails
7Coot0.98.1model fitting
19PHENIX1.2model refinementPHENIX was used to generate a model with better fit into the map
20UCSF ChimeraX1.4model refinementThe ISOLDE plugin of UCSF ChimeraX was used for further model fitting into the map and obtaining correct geometry
21Coot0.98.1model refinementCoot was used to obtain correct residue geometry
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -77 ° / Axial rise/subunit: 16.9 Å / Axial symmetry: C2
3D reconstructionResolution: 3.83 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 120943 / Symmetry type: HELICAL
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00344132
ELECTRON MICROSCOPYf_angle_d0.53359925
ELECTRON MICROSCOPYf_dihedral_angle_d4.195865
ELECTRON MICROSCOPYf_chiral_restr0.0426290
ELECTRON MICROSCOPYf_plane_restr0.0047820

+
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://pdbjlvh1.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