[English] 日本語
Yorodumi
- EMDB-51067: Beta carbonic anhydrase CsoSCA from the Halothiobacillus neapolit... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-51067
TitleBeta carbonic anhydrase CsoSCA from the Halothiobacillus neapolitanus alpha-carboxysome
Map dataPrimary map
Sample
  • Complex: Carbonic anhydrase complex
    • Protein or peptide: Immunoglobulin G-binding protein G,Carboxysome shell carbonic anhydrase
  • Ligand: ZINC ION
KeywordsCarbonic anhydrase / Carboxysome / rubisco / LYASE
Function / homology
Function and homology information


carboxysome / carbon fixation / IgG binding / carbonic anhydrase / carbonate dehydratase activity / extracellular region / metal ion binding
Similarity search - Function
Carboxysome shell carbonic anhydrase / Carboxysome shell carbonic anhydrase, N-terminal / Carboxysome shell carbonic anhydrase, C-terminal / : / : / : / Carboxysome Shell Carbonic Anhydrase, C-terminal / Carboxysome Shell Carbonic Anhydrase, catalytic domain / Carboxysome Shell Carbonic Anhydrase, N-terminal / IgG-binding B ...Carboxysome shell carbonic anhydrase / Carboxysome shell carbonic anhydrase, N-terminal / Carboxysome shell carbonic anhydrase, C-terminal / : / : / : / Carboxysome Shell Carbonic Anhydrase, C-terminal / Carboxysome Shell Carbonic Anhydrase, catalytic domain / Carboxysome Shell Carbonic Anhydrase, N-terminal / IgG-binding B / B domain / M protein-type anchor domain / GA-like domain / GA-like domain / Immunoglobulin/albumin-binding domain superfamily / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain
Similarity search - Domain/homology
Carboxysome shell carbonic anhydrase / Immunoglobulin G-binding protein G
Similarity search - Component
Biological speciesHalothiobacillus neapolitanus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.51 Å
AuthorsNg PC / Marles-Wright J / Basle A / Liu L
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)2599456 United Kingdom
CitationJournal: To Be Published
Title: Beta carbonic anhydrase CsoSCA from the Halothiobacillus neapolitanus alpha-carboxysome
Authors: Ng PC / Marles-Wright J / Basle A / Liu L
History
DepositionJul 16, 2024-
Header (metadata) releaseJul 30, 2025-
Map releaseJul 30, 2025-
UpdateJul 30, 2025-
Current statusJul 30, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_51067.png

Downloads & links

-
Map

FileDownload / File: emd_51067.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPrimary map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 256 pix.
= 275.507 Å		1.08 Å/pix.
x 256 pix.
= 275.507 Å		1.08 Å/pix.
x 256 pix.
= 275.507 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0762 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.16891192 - 0.48832244
Average (Standard dev.)-0.00026578293 (±0.01924061)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 275.5072 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_51067_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Sharpened map

Fileemd_51067_additional_1.map
AnnotationSharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map B

Fileemd_51067_half_map_1.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map A

Fileemd_51067_half_map_2.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Carbonic anhydrase complex

EntireName: Carbonic anhydrase complex
Components
  • Complex: Carbonic anhydrase complex
    • Protein or peptide: Immunoglobulin G-binding protein G,Carboxysome shell carbonic anhydrase
  • Ligand: ZINC ION

-
Supramolecule #1: Carbonic anhydrase complex

SupramoleculeName: Carbonic anhydrase complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Halothiobacillus neapolitanus (bacteria)
Molecular weightTheoretical: 409 KDa

-
Macromolecule #1: Immunoglobulin G-binding protein G,Carboxysome shell carbonic anh...

MacromoleculeName: Immunoglobulin G-binding protein G,Carboxysome shell carbonic anhydrase
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: carbonic anhydrase
Source (natural)Organism: Halothiobacillus neapolitanus (bacteria)
Molecular weightTheoretical: 68.294305 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MWSHPQFEKG GGSGGGSGGS SAWSHPQFEK YKLILNGKTL KGETTTEAVD AATAEKVFKQ YANDNGVDGE WTYDDATKTF TVTEPMSDY DIPTTENLYF QGNTRNTRSK QRAPFGVSSS VKPRLDLIEQ APNPAYDRHP ACITLPERTC RHPLTDLEAN E QLGRCEDS ...String:
MWSHPQFEKG GGSGGGSGGS SAWSHPQFEK YKLILNGKTL KGETTTEAVD AATAEKVFKQ YANDNGVDGE WTYDDATKTF TVTEPMSDY DIPTTENLYF QGNTRNTRSK QRAPFGVSSS VKPRLDLIEQ APNPAYDRHP ACITLPERTC RHPLTDLEAN E QLGRCEDS VKNRFDRVIP FLQVVAGIPL GLDYVTRVQE LAQSSLGHTL PEELLKDNWI SGHNLKGIFG YATAKALTAA TE QFSRKIM SEKDDSASAI GFFLDCGFHA VDISPCADGR LKGLLPYILR LPLTAFTYRK AYAGSMFDIE DDLAQWEKNE LRR YREGVP NTADQPTRYL KIAVYHFSTS DPTHSGCAAH GSNDRAALEA ALTQLMKFRE AVENAHCCGA SIDILLIGVD TDTD AIRVH IPDSKGFLNP YRYVDNTVTY AQTLHLAPDE ARVIIHEAIL NANRSDGWAK GNGVASEGMR RFIGQLLINN LSQID YVVN RHGGRYPPND IGHAERYISV GDGFDEVQIR NLAYYAHLDT VEENAIDVDV GIKIFTKLNL SRGLPIPIAI HYRYDP NVP GSRERTVVKA RRIYNAIKER FSSLDEQNLL QFRLSVQAQD IGSPIEEVAS A

UniProtKB: Immunoglobulin G-binding protein G, Carboxysome shell carbonic anhydrase

-
Macromolecule #2: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 2 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1.5 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
100.0 mMTris/HClTris/Hydrochloric acid
150.0 mMNaClSodium chloride
1.0 mMEDTAEthylenediaminetetraacetic acid
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.026000000000000002 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 240000
Sample stageCooling holder cryogen: NITROGEN

+
Image processing

Particle selectionNumber selected: 1390946
Details: Blob picker with 150 A diameter. Picks verified using inspect picks job.
CTF correctionSoftware - Name: cryoSPARC (ver. 4.5) / Details: Patch CTF in cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: Ab initio asymmetric model / Details: Ab initio job in cryoSPARC
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: D3 (2x3 fold dihedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.51 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5) / Details: Homogeneous refinement in cryoSPARC / Number images used: 435319
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5) / Details: Homogeneous refinement
Final 3D classificationNumber classes: 2 / Avg.num./class: 200000 / Software - Name: cryoSPARC (ver. 4.5) / Details: 3D classification with 2 classes
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
DetailsModel fitting using ChimeraX
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Cross-correlation coefficient
Output model

PDB-9g4t:
Beta carbonic anhydrase CsoSCA from the Halothiobacillus neapolitanus alpha-carboxysome

+
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