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- EMDB-0020: Hexameric cytochrome c nitrite reductase from the bacterium Thioa... -

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Basic information

Entry
Database: EMDB / ID: EMD-0020
TitleHexameric cytochrome c nitrite reductase from the bacterium Thioalkalivibrio nitratireducens (TvNiR)
Map dataCytochrome c nitrite reductase from the bacterium Thioalkalivibrio nitratireducens (TvNiR).
Sample
  • Complex: Cytochrome c nitrite reductase from the bacterium Thioalkalivibrio nitratireducens (TvNiR)
    • Protein or peptide: cytochrome c nitrite reductase
Biological speciesThioalkalivibrio nitratireducens (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.56 Å
AuthorsBaymukhametov TN / Chesnokov YM / Pichkur EB / Boyko KM / Tikhonova TV / Myasnikov AG / Vasiliev AL / Lipkin AV / Popov VO / Kovalchuk MV
CitationJournal: Acta Naturae / Year: 2018
Title: Three-Dimensional Structure of Cytochrome c Nitrite Reductase As Determined by Cryo-Electron Microscopy.
Authors: T N Baymukhametov / Y M Chesnokov / E B Pichkur / K M Boyko / T V Tikhonova / A G Myasnikov / A L Vasiliev / A V Lipkin / V O Popov / M V Kovalchuk /
Abstract: The structure of cytochrome c nitrite reductase from the bacterium Thioalkalivibrio nitratireducens was determined by cryo-electron microscopy (cryo-EM) at a 2.56 Å resolution. Possible structural ...The structure of cytochrome c nitrite reductase from the bacterium Thioalkalivibrio nitratireducens was determined by cryo-electron microscopy (cryo-EM) at a 2.56 Å resolution. Possible structural heterogeneity of the enzyme was assessed. The backbone and side-chain orientations in the cryo-EM-based model are, in general, similar to those in the high-resolution X-ray diffraction structure of this enzyme.
History
DepositionMay 18, 2018-
Header (metadata) releaseMay 23, 2018-
Map releaseJan 30, 2019-
UpdateJan 30, 2019-
Current statusJan 30, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.23
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.23
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0020.png

Downloads & links

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Map

FileDownload / File: emd_0020.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCytochrome c nitrite reductase from the bacterium Thioalkalivibrio nitratireducens (TvNiR).
Voxel sizeX=Y=Z: 0.86 Å
Density
Contour LevelBy AUTHOR: 0.23 / Movie #1: 0.23
Minimum - Maximum-0.921547 - 1.6588855
Average (Standard dev.)0.0027781222 (±0.061088625)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 220.16 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.860.860.86
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z220.160220.160220.160
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.9221.6590.003

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Supplemental data

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Sample components

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Entire : Cytochrome c nitrite reductase from the bacterium Thioalkalivibri...

EntireName: Cytochrome c nitrite reductase from the bacterium Thioalkalivibrio nitratireducens (TvNiR)
Components
  • Complex: Cytochrome c nitrite reductase from the bacterium Thioalkalivibrio nitratireducens (TvNiR)
    • Protein or peptide: cytochrome c nitrite reductase

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Supramolecule #1: Cytochrome c nitrite reductase from the bacterium Thioalkalivibri...

SupramoleculeName: Cytochrome c nitrite reductase from the bacterium Thioalkalivibrio nitratireducens (TvNiR)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Hexameric form
Source (natural)Organism: Thioalkalivibrio nitratireducens (bacteria)

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Macromolecule #1: cytochrome c nitrite reductase

MacromoleculeName: cytochrome c nitrite reductase / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO / EC number: nitrite reductase (cytochrome; ammonia-forming)
Source (natural)Organism: Thioalkalivibrio nitratireducens (bacteria)
SequenceString: MNDLNRLGRV GRWIAGAACL FLASAAHAEP GENLKPVDAM QCFDCHTQIE DMHTVGKHAT VNCVHCHDAT EHVETASSRR MGERPVTRMD LEACATCHTA QFNSFVEVRH ESHPRLEKAT PTSRSPMFDK LIAGHGFAFE HAEPRSHAFM LVDHFVVDRA YGGRFQFKNW ...String:
MNDLNRLGRV GRWIAGAACL FLASAAHAEP GENLKPVDAM QCFDCHTQIE DMHTVGKHAT VNCVHCHDAT EHVETASSRR MGERPVTRMD LEACATCHTA QFNSFVEVRH ESHPRLEKAT PTSRSPMFDK LIAGHGFAFE HAEPRSHAFM LVDHFVVDRA YGGRFQFKNW QKVTDGMGAV RGAWTVLTDA DPESSDQRRF LSQTATAANP VCLNCKTQDH ILDWAYMGDE HEAAKWSRTS EVVEFARDLN HPLNCFMCHD PHSAGPRVVR DGLINAVVDR GLGTYPHDPV KSEQQGMTKV TFQRGREDFR AIGLLDTADS NVMCAQCHVE YNCNPGYQLS DGSRVGMDDR RANHFFWANV FDYKEAAQEI DFFDFRHATT GAALPKLQHP EAETFWGSVH ERNGVACADC HMPKVQLENG KVYTSHSQRT PRDMMGQACL NCHAEWTEDQ ALYAIDYIKN YTHGKIVKSE YWLAKMIDLF PVAKRAGVSE DVLNQARELH YDAHLYWEWW TAENSVGFHN PDQARESLMT SISKSKEAVS LLNDAIDAQV ASR

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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: 7
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.026 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 98 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 75000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Frames/image: 1-30 / Number real images: 3055 / Average electron dose: 3.3 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: Gctf (ver. 1.18)
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final reconstructionApplied symmetry - Point group: D3 (2x3 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 2.56 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 33891

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT

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