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- EMDB-31446: Cryo-EM map of Rhizobium etli MprF with the improved density of t... -
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Open data
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Basic information
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Title | Cryo-EM map of Rhizobium etli MprF with the improved density of the aa-PGS domain | |||||||||
![]() | 3.3 A Refine3D map | |||||||||
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Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Nishimura 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 | |||||||||
![]() | ![]() Title: to be published Authors: Nishimura M | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 23.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 16.9 KB 16.9 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 8.6 KB | Display | ![]() |
Images | ![]() | 144 KB | ||
Masks | ![]() | 28.7 MB | ![]() | |
Others | ![]() ![]() | 24.1 MB 24.1 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | 3.3 A Refine3D map | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.996 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_31446_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_31446_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : MprF
Entire | Name: MprF |
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Components |
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-Supramolecule #1: MprF
Supramolecule | Name: MprF / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 187 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
-Macromolecule #1: MprF
Macromolecule | Name: MprF / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Recombinant expression | Organism: ![]() ![]() ![]() |
Sequence | String: 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 |
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation
Concentration | 6 mg/mL | |||||||||||||||
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Buffer | pH: 8 Component:
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Grid | Model: 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 | |||||||||||||||
Vitrification | Cryogen 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
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Specialist optics | Energy filter - Name: GIF Bioquantum |
Details | CDS mode |
Image recording | Film 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 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |