[English] 日本語
Yorodumi
- EMDB-11158: Cryo-EM structure of the nitrilase from Pseudomonas fluorescens E... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-11158
TitleCryo-EM structure of the nitrilase from Pseudomonas fluorescens EBC191 at 3.3 Angstroms
Map data
Sample
  • Complex: Active helical nitrilase homooligomer
    • Protein or peptide: NitA
Keywordsbacterial nitrilase / arylacetonitrilase / hydrolase
Function / homology
Function and homology information


nitrilase activity / detoxification of nitrogen compound / nitrile hydratase 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 speciesPseudomonas fluorescens (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsEppinger E / Stolz A
CitationJournal: To Be Published
Title: Cryo-EM structure of the nitrilase from Pseudomonas fluorescens EBC191 at 3.3 Angstroms
Authors: Eppinger E / Stolz A / Sewell BT
History
DepositionJun 9, 2020-
Header (metadata) releaseJun 30, 2021-
Map releaseJun 30, 2021-
UpdateMay 1, 2024-
Current statusMay 1, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6zby
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6zby
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11158.png

Downloads & links

-
Map

FileDownload / File: emd_11158.map.gz / Format: CCP4 / Size: 9.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 147 pix.
= 154.056 Å		1.05 Å/pix.
x 131 pix.
= 137.288 Å		1.05 Å/pix.
x 133 pix.
= 139.384 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.048 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.082405895 - 0.13379925
Average (Standard dev.)0.0023105105 (±0.013520567)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin858470
Dimensions131133147
Spacing133131147
CellA: 139.384 Å / B: 137.288 Å / C: 154.056 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0481.0481.048
M x/y/z133131147
origin x/y/z0.0000.0000.000
length x/y/z139.384137.288154.056
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS848570
NC/NR/NS133131147
D min/max/mean-0.0820.1340.002

-
Supplemental data

-
Sample components

-
Entire : Active helical nitrilase homooligomer

EntireName: Active helical nitrilase homooligomer
Components
  • Complex: Active helical nitrilase homooligomer
    • Protein or peptide: NitA

-
Supramolecule #1: Active helical nitrilase homooligomer

SupramoleculeName: Active helical nitrilase homooligomer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Pseudomonas fluorescens (bacteria) / Strain: EBC191

-
Macromolecule #1: NitA

MacromoleculeName: NitA / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas fluorescens (bacteria)
Molecular weightTheoretical: 37.740746 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MTVHKKQYKV AAVQAAPAFL DLEAGVAKAI GLIAQAAAEG ASLVAFPEAW LPGYPWWIWL DSPAGGMRFV QRNFDNALEV GSEPFERLC RAAAQHKIYV VLGFTERSGG TLYLAQAIID DCGRVVATRR KLKPTHVERS VYGEGDGSDL AVHDTTLGRL G ALCCAEHI ...String:
MTVHKKQYKV AAVQAAPAFL DLEAGVAKAI GLIAQAAAEG ASLVAFPEAW LPGYPWWIWL DSPAGGMRFV QRNFDNALEV GSEPFERLC RAAAQHKIYV VLGFTERSGG TLYLAQAIID DCGRVVATRR KLKPTHVERS VYGEGDGSDL AVHDTTLGRL G ALCCAEHI QPLSKYAMYA QHEQVHIAAW PSFSVYRGAA FQLSAQANNA ASQVYALEGQ CFVLAPCATV SKEMLDELID SP AKAELLL EGGGFAMIYG PDGAPLCTPL AETEEGILYA DIDLGVIGVA KAAYDPVGHY SRPDVLRLLV NREPMTRVHY VQP QSLPET SVLAFGAGAD AIRSEENPEE QGDK

UniProtKB: NitA

-
Experimental details

-
Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

-
Sample preparation

Concentration0.15 mg/mL
BufferpH: 7.8
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK I
Details: The sample (2.5 ul) was applied to the grid and incubated for 30 seconds at 100% humidity before blotting and plunging..

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Number real images: 2929 / Average exposure time: 6.0 sec. / Average electron dose: 43.1 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 16.36 Å
Applied symmetry - Helical parameters - Δ&Phi: -67.31 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 91429
Segment selectionNumber selected: 278053 / Software - Name: RELION (ver. 3.1)
Startup modelType of model: INSILICO MODEL / In silico model: featureless cylinder
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL / Target criteria: Cross-correlation coefficient
Output model

PDB-6zby:
Cryo-EM structure of the nitrilase from Pseudomonas fluorescens EBC191 at 3.3 Angstroms

+
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