[English] 日本語
Yorodumi
- PDB-9er3: Cyanide dihydratase from Bacillus pumilus C1 E155R variant with a... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9er3
TitleCyanide dihydratase from Bacillus pumilus C1 E155R variant with altered helical twist.
ComponentsCyanide dihydratase
KeywordsHYDROLASE / Left-handed helix.
Function / homologyNitrilase/Cyanide hydratase / Nitrilases / cyanide hydratase signature 1. / Nitrilase/cyanide hydratase, conserved site / nitrilase activity / Carbon-nitrogen hydrolase superfamily / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase domain profile. / Carbon-nitrogen hydrolase / Cyanide dihydratase
Function and homology information
Biological speciesBacillus pumilus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsDlamini, L.S. / Woodward, J.D. / Sewell, B.T.
Funding support South Africa, 1items
OrganizationGrant numberCountry
National Research Foundation in South Africa South Africa
CitationJournal: To Be Published
Title: Cyanide dihydratase from Bacillus pumilus C1 E155R variant with altered helical twist
Authors: Dlamini, L.S. / Woodward, J.D. / Sewell, B.T.
History
DepositionMar 22, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
S: Cyanide dihydratase
H: Cyanide dihydratase
L: Cyanide dihydratase
B: Cyanide dihydratase
A: Cyanide dihydratase
D: Cyanide dihydratase
M: Cyanide dihydratase
F: Cyanide dihydratase
G: Cyanide dihydratase
K: Cyanide dihydratase
I: Cyanide dihydratase
C: Cyanide dihydratase
N: Cyanide dihydratase
E: Cyanide dihydratase
O: Cyanide dihydratase
P: Cyanide dihydratase
J: Cyanide dihydratase
R: Cyanide dihydratase
T: Cyanide dihydratase


Theoretical massNumber of molelcules
Total (without water)687,77619
Polymers687,77619
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

#1: Protein
Cyanide dihydratase


Mass: 36198.730 Da / Num. of mol.: 19
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: single particle reconstruction

-
Sample preparation

ComponentName: Cyanide dihydratase from Bacillus pumilus C1 E155R variant with altered helical twist.
Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.703 MDa / Experimental value: NO
Source (natural)Organism: Bacillus pumilus (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4 / Details: 50 mM NaCL, 50 mM Tris-HCl
Buffer componentConc.: 50 mM / Name: Tris-(hydroxymethyl) aminomethane / Formula: Tris-HCl
SpecimenConc.: 1.8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 2.04 sec. / Electron dose: 1 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 31418

-
Processing

EM software
IDNameVersionCategoryDetails
1RELION4.0.1particle selection
2EPU3.5.1image acquisition
4RELION4.0.1CTF correction
7PHENIX1.2105207model fitting
10RELION4.0.1final Euler assignment
12RELION4.0.13D reconstruction
13PHENIX1.2105207model refinementreal space refine
14UCSF ChimeraX1.6.1model refinementISOLDE plugin
15Coot0.9.8.1model refinementReal space refine and rotamer fitting
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2387974
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 200866 / Algorithm: FOURIER SPACE / Num. of class averages: 50 / Symmetry type: POINT
Atomic model buildingB value: 101.248 / Protocol: AB INITIO MODEL / Space: REAL / Target criteria: Cross-correlation coefficient
Atomic model buildingDetails: The initial model was built ab initio using the map and amino acid sequence.
Source name: Other / Type: other
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00549685
ELECTRON MICROSCOPYf_angle_d0.52767469
ELECTRON MICROSCOPYf_dihedral_angle_d6.1776662
ELECTRON MICROSCOPYf_chiral_restr0.0437087
ELECTRON MICROSCOPYf_plane_restr0.0058816

+
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