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- EMDB-3718: 3,4-dihydroxybenzoate decarboxylase AroY from Enterobacter cloaca... -

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Basic information

Entry
Database: EMDB / ID: 3718
Title3,4-dihydroxybenzoate decarboxylase AroY from Enterobacter cloacae in the apo state
Sample3,4-dihydroxybenzoate decarboxylase
SourceEnterobacter cloacae / bacteria / エンテロバクター・クロアカエ
Map dataSingle-particle cryo-EM map of the 3,4-dihydroxybenzoate decarboxylase AroY from Enterobacter cloacae in the apo state.
Methodsingle particle reconstruction, at 4.6 Å resolution
AuthorsBaerland N / Kaltwasser S / Vonck J / Pavkov-Keller T
CitationAngew. Chem. Int. Ed. Engl., 2017

Angew. Chem. Int. Ed. Engl., 2017 StrPapers
Regioselective para-Carboxylation of Catechols by a Prenylated Flavin Dependent Decarboxylase.
Stefan Payer / Stephen A Marshall / Natalie Bärland / Xiang Sheng / Tamara Reiter / Andela Dordic / Georg Steinkellner / Christiane Wuensch / Susann Kaltwasser / Karl Fisher / Stephen E J Rigby / Peter Macheroux / Janet Vonck / Karl Gruber / Kurt Faber / Fahmi Himo / David Leys / Tea Pavkov-Keller / Silvia M Glueck

DateDeposition: May 12, 2017 / Header (metadata) release: May 31, 2017 / Map release: Sep 13, 2017 / Last update: Sep 13, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.02
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

Downloads & links

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Map

Fileemd_3718.map.gz (map file in CCP4 format, 44958 KB)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
224 pix
1.12 Å/pix.
= 250.88 Å
224 pix
1.12 Å/pix.
= 250.88 Å
224 pix
1.12 Å/pix.
= 250.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.12 Å
Density
Contour Level:0.02 (by author), 0.02 (movie #1):
Minimum - Maximum-0.037165664 - 0.06892177
Average (Standard dev.)-0.00015808595 (0.0039911764)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions224224224
Origin000
Limit223223223
Spacing224224224
CellA=B=C: 250.88 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.121.121.12
M x/y/z224224224
origin x/y/z0.0000.0000.000
length x/y/z250.880250.880250.880
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS224224224
D min/max/mean-0.0370.069-0.000

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Supplemental data

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Sample components

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Entire 3,4-dihydroxybenzoate decarboxylase

EntireName: 3,4-dihydroxybenzoate decarboxylase / Number of components: 2
MassTheoretical: 320 kDa

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Component #1: protein, 3,4-dihydroxybenzoate decarboxylase

ProteinName: 3,4-dihydroxybenzoate decarboxylase / Recombinant expression: No
MassTheoretical: 320 kDa
SourceSpecies: Enterobacter cloacae / bacteria / エンテロバクター・クロアカエ
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #2: protein, 3,4-dihydroxybenzoate decarboxylase

ProteinName: 3,4-dihydroxybenzoate decarboxylase / Recombinant expression: No

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 0.15 mg/ml / pH: 7.5
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 283 K / Humidity: 100 % / Details: 11 second blot

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Electron microscopy imaging

ImagingMicroscope: JEOL 3200FSC
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 54 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 30000 X (nominal), 44643 X (calibrated) / Cs: 4.2 mm / Imaging mode: BRIGHT FIELD / Energy filter: JEOL in-column filter with a width of 20eV
Specimen HolderModel: JEOL 3200FSC CRYOHOLDER
CameraDetector: GATAN K2 (4k x 4k)

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Image acquisition

Image acquisitionDetails: 40-frame movies in 8 seconds

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: D3 (2*3 fold dihedral) / Number of projections: 22650
3D reconstructionSoftware: RELION / Resolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution assessment)

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