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- EMDB-31446: Cryo-EM map of Rhizobium etli MprF with the improved density of t... -

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Basic information

Entry
Database: EMDB / ID: EMD-31446
TitleCryo-EM map of Rhizobium etli MprF with the improved density of the aa-PGS domain
Map data3.3 A Refine3D map
Sample
  • Organelle or cellular component: MprF
    • Protein or peptide: MprF
Biological speciesRhizobium etli CFN 42 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.27 Å
AuthorsNishimura M / Hirano H / Kobayashi K / Gill CP / Phan CNK / Kise Y / Kusakizako T / Yamashita K / Ito Y / Roy H ...Nishimura M / Hirano H / Kobayashi K / Gill CP / Phan CNK / Kise Y / Kusakizako T / Yamashita K / Ito Y / Roy H / Nishizawa T / Nureki O
CitationJournal: To Be Published
Title: to be published
Authors: Nishimura M
History
DepositionJun 17, 2021-
Header (metadata) releaseJun 22, 2022-
Map releaseJun 22, 2022-
UpdateJun 22, 2022-
Current statusJun 22, 2022Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_31446.png

Downloads & links

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Map

FileDownload / File: emd_31446.map.gz / Format: CCP4 / Size: 28.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3.3 A Refine3D map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1 Å/pix.
x 196 pix.
= 195.216 Å		1 Å/pix.
x 196 pix.
= 195.216 Å		1 Å/pix.
x 196 pix.
= 195.216 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.996 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0188
Minimum - Maximum-0.014026689 - 0.05446233
Average (Standard dev.)0.00076325255 (±0.0044068117)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions196196196
Spacing196196196
CellA=B=C: 195.216 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_31446_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_31446_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_31446_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : MprF

EntireName: MprF
Components
  • Organelle or cellular component: MprF
    • Protein or peptide: MprF

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Supramolecule #1: MprF

SupramoleculeName: MprF / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Rhizobium etli CFN 42 (bacteria)
Molecular weightTheoretical: 187 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant strain: DE3 / Recombinant plasmid: pTSP1

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Macromolecule #1: MprF

MacromoleculeName: MprF / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhizobium etli CFN 42 (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSGHGNLEEM EATDGFSFRT LFRRYRTPLT AAATLIVFCL VGYAIMQLTN EVRYDDVVAA LAATGPSAIL LALFFTALSF LSLVFYDLNA IEYIGKKLPF PHVALTAFSA YAVGNTAGFG ALSGGAIRYR AYTRLGLSPE DIGRIIAFVT LSFGLGLAAV ASIALIIIAS ...String:
MSGHGNLEEM EATDGFSFRT LFRRYRTPLT AAATLIVFCL VGYAIMQLTN EVRYDDVVAA LAATGPSAIL LALFFTALSF LSLVFYDLNA IEYIGKKLPF PHVALTAFSA YAVGNTAGFG ALSGGAIRYR AYTRLGLSPE DIGRIIAFVT LSFGLGLAAV ASIALIIIAS EIGPLIGVSP FLLRLIAGSI IAILGAVMII GREGRVLNFG AVAIRLPDSR TWSRQFLVTA FDIAASASVL YVLLPQTAIG WPVFLAVYAI AVGLGVLSHV PAGLGVFETV IIASLGSAVN IDAVLGSLVL YRLIYHVLPL LIAVLAVSAA ELRRFVDHPA ASSVRRIGGR LMPQLLSTLA LLLGVMLVFS SVTPTPDQNL EFLSNYLPLP MVEGAHFLSS LLGLALVVAA RGLGQRLDGA WWVAVFSAVA ALTLSLLKAI ALVEAAFLAF LIFGLFVSRR LFTRHASLLN QAMTASWLMA IAVIVVGAVV ILLFVYRDVE YSNELWWQFE FTAEAPRGLR ALLGITIISS AIAIFSLLRP ATFRPEPATE EALTRAVEIV RKQGNADANL VRMGDKSIMF SEKGDAFIMY GRQGRSWIAL FDPVGDHGAV QELVWRFVEA ARAAGCRAVF YQISPALLSH CADAGLRAFK LGELAVADLR TFEMKGGKWA NLRQTASRAQ RDGLEFAVVE PENVPDIIDE LAAVSTAWLE HHNAKEKGFS LGSFDPDYVS AQPVGILKKD GKIVAFANIL VTESKEEGTI DLMRFSPDAP KGSMDFLFVQ IMEYLRNQGF THFNLGMAPL SGMSKREAAP VWDRIGSTVF EHGERFYNFK GLRAFKSKFH PHWQPRYLAV SGGGNPMIAL MDATFLIGGG LKGVVRK

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration6 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMC4H11NO3-HClTris-HCl
150.0 mMNaClsodium chloride
0.06 %C56H92O25GDN
100.0 uMC9H15O6PTCEP
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Details: a waiting time of 10 s and a blotting time of 4 s
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: waiting time of 10 s and blotting time of 4 s.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum
DetailsCDS mode
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 3159 / Average exposure time: 5.0 sec. / Average electron dose: 56.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.27 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 76852
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationSoftware - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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