[English] 日本語
Yorodumi
- EMDB-32357: Dimethylformamidase, 2x(A2B2) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-32357
TitleDimethylformamidase, 2x(A2B2)
Map dataB-factor sharpened map from post processing step in Relion
Sample
  • Complex: DMFase, an amidohydrolase
    • Protein or peptide: N,N-dimethylformamidase large subunit
    • Protein or peptide: N,N-dimethylformamidase small subunit
  • Ligand: FE (III) ION
  • Ligand: water
KeywordsAmidohydrolase / mononuclear iron / AB polypeptide / tetramer / HYDROLASE
Function / homologyN,N-dimethylformamidase / N,N-dimethylformamidase activity / N,N-dimethylformamidase beta subunit-like, C-terminal / N,N-dimethylformamidase beta subunit-like, C-terminal / Concanavalin A-like lectin/glucanase domain superfamily / metal ion binding / N,N-dimethylformamidase large subunit / N,N-dimethylformamidase small subunit
Function and homology information
Biological speciesParacoccus sp. (bacteria) / Paracoccus sp. SSG05 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsVinothkumar KR / Subramanian R
Funding support India, 1 items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)DBT/PR12422/MED/31/287/2014 India
CitationJournal: To Be Published
Title: Dimethylformamidase with a Unique Iron Center
Authors: Arya C / Ramanathan G / Vinothkumar KR / Subramanian R
History
DepositionDec 7, 2021-
Header (metadata) releaseApr 6, 2022-
Map releaseApr 6, 2022-
UpdateJun 26, 2024-
Current statusJun 26, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_32357.png

Downloads & links

-
Map

FileDownload / File: emd_32357.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationB-factor sharpened map from post processing step in Relion
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 320 pix.
= 342.4 Å		1.07 Å/pix.
x 320 pix.
= 342.4 Å		1.07 Å/pix.
x 320 pix.
= 342.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.09
Minimum - Maximum-0.19257833 - 0.39406684
Average (Standard dev.)0.0000274257 (±0.017593727)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 342.40002 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: One of the half maps from final refinement

Fileemd_32357_half_map_1.map
AnnotationOne of the half maps from final refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: One of the half maps from final refinement

Fileemd_32357_half_map_2.map
AnnotationOne of the half maps from final refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : DMFase, an amidohydrolase

EntireName: DMFase, an amidohydrolase
Components
  • Complex: DMFase, an amidohydrolase
    • Protein or peptide: N,N-dimethylformamidase large subunit
    • Protein or peptide: N,N-dimethylformamidase small subunit
  • Ligand: FE (III) ION
  • Ligand: water

-
Supramolecule #1: DMFase, an amidohydrolase

SupramoleculeName: DMFase, an amidohydrolase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Paracoccus sp. (bacteria) / Strain: SSG05
Molecular weightTheoretical: 400 KDa

-
Macromolecule #1: N,N-dimethylformamidase large subunit

MacromoleculeName: N,N-dimethylformamidase large subunit / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: N,N-dimethylformamidase
Source (natural)Organism: Paracoccus sp. SSG05 (bacteria)
Molecular weightTheoretical: 86.341758 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MKDIAIRGYC DRPSVATGET IRFYVSANET RGTFDAELVR LIHGDSNPAG PGYKEEAIKS DLEGQYPARF QRTQFGSYVE VADPDAGLQ PDGAFSVHLF LWSTTPSRGR QGIASRWNDE RQSGWNLAIE DGRVVFTIGD GSGATSSVVS DRPLFQQIWY S ITGVYDPE ...String:
MKDIAIRGYC DRPSVATGET IRFYVSANET RGTFDAELVR LIHGDSNPAG PGYKEEAIKS DLEGQYPARF QRTQFGSYVE VADPDAGLQ PDGAFSVHLF LWSTTPSRGR QGIASRWNDE RQSGWNLAIE DGRVVFTIGD GSGATSSVVS DRPLFQQIWY S ITGVYDPE KKQLRLYQKS VVNRTNSRFG LVVPLDSDCA VSADATVKAA DSETSLLIAG LGEAAAQDGR TWCIAHYNGK VD APKIYGC ALGQDDAEKL SRGEIVRPIS RLAHWDFSAG IGLNGIPTDH VVDASGYGHH GRCMNQPSRG STGWNWDGHE ENF IHCPEQ YGALWFHEDC LDDCRWEKDF EFTVPEGLKS DFYAVKIRYE DTEDYIPFFV LPPRGTATAP ILVIASTLSY LAYA NEQIM HKADIGQAVA GHTPVLNEND VELHKNLSYY GLSTYDGHID GRGVQYTSWR RPIMNLRPKH RQGFGSIWEL PADLH LIDW LNHNGFEYDV ATEHDLNDQG AELLRRYKVV LTGSHPEYQT WANADAWEDY LADGGRGMYL AANGMYWIVE VHPEKP WVM EVRKELGVTA WEAPPGEYHY STNGRRGGRF RGRARATQKI WGTGMSSFGF DHSGYFVQMP DSQDERVAWI MEGIDPE ER IGDGGLVGGG AGGYELDRYD LALGTPPNTL LLASSVEHSV VYTVIPDDKA FPHPGMNGGE HPFVRADITY FSTANGGG M FATSSISWLG SLSWNDYDNN VSKMTKNVLN QFIKDEPAPR VKLAAALEHH HHHH

UniProtKB: N,N-dimethylformamidase large subunit

-
Macromolecule #2: N,N-dimethylformamidase small subunit

MacromoleculeName: N,N-dimethylformamidase small subunit / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO / EC number: N,N-dimethylformamidase
Source (natural)Organism: Paracoccus sp. SSG05 (bacteria)
Molecular weightTheoretical: 16.083823 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MTEASESCVR DPSNYRDRSA DWYAFYDERR RKEIIDIIDE HPEIVEEHAA NPFGYRKHPS PYLQRVHNYF RMQPTFGRYY IYSEREWDA YRIATIREFG ELPELGDERF KTEEEAMHAV FLRRIEDVRA ELA

UniProtKB: N,N-dimethylformamidase small subunit

-
Macromolecule #3: FE (III) ION

MacromoleculeName: FE (III) ION / type: ligand / ID: 3 / Number of copies: 4 / Formula: FE
Molecular weightTheoretical: 55.845 Da

-
Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 290 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration5 mg/mL
BufferpH: 7.2
Component:
ConcentrationNameFormula
25.0 mMHepes
200.0 mMSodium ChlorideNaCl
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 291 K / Instrument: FEI VITROBOT MARK IV / Details: wait time - 10 seconds and 3.5 seconds blot.
DetailsEnzyme after gel filtration was used for cryoEM grid prep. Sample was held at 37 degrees before application on the grid.

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 79.0 K
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 548 / Average exposure time: 60.0 sec. / Average electron dose: 28.3 e/Å2
Details: One image was collected per hole. Total of 25 frames was saved and each frame has ~1.13 e/A2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated magnification: 130841 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.2 µm / Nominal defocus min: 0.85 µm / Nominal magnification: 75000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

DetailsFrom the 548 images, MotionCor2 was used for full frame alignment. After CTF estimation, 528 micrographs were selected and used for further extraction. Two rounds of 2D classification of extracted particles resulted in 30689 particles and used for refinement.
Particle selectionNumber selected: 114182
Startup modelType of model: OTHER
Details: Previous EM map (obtained from 2D classes and angular reconstitution with EMAN2) was low pass filtered to 60A.
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1)
Details: The final reconstruction was from a single 3D class after B-factor weighting and aberration correction in Relion 3.1
Number images used: 28964
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationNumber classes: 5 / Software - Name: RELION (ver. 3.1)
Details: Resolution was limited to 6A and T=4. One good class with predominant number of particles were taken to the next step of refinement and reconstruction.
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial model
PDB IDChain

6lvb

chain_id: A, source_name: PDB, initial_model_type: experimental model

6lvb

chain_id: B, source_name: PDB, initial_model_type: experimental model
DetailsServalcat was used along with Refmac to calculate fofc maps and extensively used for modelling.
RefinementSpace: RECIPROCAL / Protocol: OTHER / Overall B value: 73.98
Output model

PDB-7w8j:
Dimethylformamidase, 2x(A2B2)

+
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