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- EMDB-5437: dATP-inhibited class Ia ribonucleotide reductase from E. coli: al... -

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Basic information

Entry
Database: EMDB / ID: 5437
TitledATP-inhibited class Ia ribonucleotide reductase from E. coli: alpha4beta4 open conformation 7
Keywordsribonucleotide reductase / allostery / inhibition / nucleotide metabolism
SampleE. coli Class Ia ribonucleotide reductase
SourceEscherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Map dataalpha4beta4 open conformation 7
Methodsingle particle reconstruction, at 33.1 A resolution
AuthorsZimanyi CM / Ando N / Brignole E / Asturias FJ / Stubbe J / Drennan CL
CitationStructure, 2012, 20, 1374-1383

Structure, 2012, 20, 1374-1383 StrPapers
Tangled up in knots: structures of inactivated forms of E. coli class Ia ribonucleotide reductase.
Christina M Zimanyi / Nozomi Ando / Edward J Brignole / Francisco J Asturias / Joanne Stubbe / Catherine L Drennan

DateDeposition: Jun 13, 2012 / Header (metadata) release: Jul 13, 2012 / Map release: Jul 25, 2012 / Last update: Jun 13, 2012

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.88
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1.88
  • Imaged by UCSF CHIMERA
  • Download
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Map

Fileemd_5437.map.gz (map file in CCP4 format, 1459 KB)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
72 pix
6.54 A/pix
= 470.88 A
72 pix
4.36 A/pix
= 313.92 A
72 pix
4.36 A/pix
= 313.92 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

(generated in cubic-lattice coordinate)

Voxel sizeX: 4.36 A / Y: 4.36 A / Z: 6.54 A
Density
Contour Level:1.88 (by author), 1.88 (movie #1):
Minimum - Maximum-4.68228865 - 8.78501797
Average (Standard dev.)0.02093046 (0.66588986)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions727272
Origin000
Limit717171
Spacing727272
CellA: 313.92 A / B: 313.92 A / C: 470.88 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/pix X/Y/Z4.364.366.54
M x/y/z727272
origin x/y/z0.0000.0000.000
length x/y/z313.920313.920470.880
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-150-1500
NX/NY/NZ301301151
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS727272
D min/max/mean-4.6828.7850.021

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Supplemental data

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Sample components

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Entire E. coli Class Ia ribonucleotide reductase

EntireName: E. coli Class Ia ribonucleotide reductase / Number of components: 1
Oligomeric State: two alpha2 subunits in complex with two beta2 subunits
MassTheoretical: 517 kDa / Experimental: 517 kDa
Measured by: Calculated from amino acid sequence of subunits

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Component #1: protein, E. coli Class Ia ribonucleotide reductase

ProteinName: E. coli Class Ia ribonucleotide reductase / a.k.a: RNR / Oligomeric Details: hetero-octamer / Details: alpha4beta4 open conformation / Recombinant expression: Yes / Number of Copies: 1
MassTheoretical: 517 kDa / Experimental: 517 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
External referencesGene Ontology: GO: 0005971

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionBuffer solution: 50 mM HEPES, 15 mM MgCl2, 1 mM EDTA, 1 mM CDP, 0.05 mM dATP
pH: 7.6
Support filmthin carbon support on 300 mesh Cu/Rh grid, glow discharge in amylamine
Staining5ul protein, washed immediately 3x [2% uranyl acetate, 0.2% trehalose], carbon sandwich
VitrificationInstrument: NONE / Cryogen name: NONE

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Electron microscopy imaging

ImagingMicroscope: FEI TECNAI F20 / Date: Jul 31, 2010
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 120 kV / Electron dose: 25 e/A2 / Illumination mode: FLOOD BEAM
LensMagnification: 50000 X (nominal) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 275 - 1801 nm
Specimen HolderHolder: room temperature / Model: SIDE ENTRY, EUCENTRIC / Tilt Angle: -59.1 - -54.3 deg.
CameraDetector: GATAN ULTRASCAN 4000 (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 89 / Bit depth: 16 / Details: images acquired as tilt-pairs

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 257
Details: Semi-automated particle selection from untilted images with EMAN2. Particles matched in tilted images using modified TiltPicker. Processed in SPIDER.
Applied symmetry: C1 (asymmetric)
3D reconstructionAlgorithm: random conical tilt / Software: SPIDER / CTF correction: each particle / Resolution: 33.1 A / Resolution method: FSC 0.5

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Atomic model buiding

Modeling #1Software: Chimera / Refinement protocol: rigid body / Target criteria: correlation / Refinement space: REAL
Details: Protocol: rigid body. Subunits iteratively fit with Chimera
Input PDB model: 4R1R
Chain ID: A, B, D, E
Modeling #2Software: Chimera / Refinement protocol: rigid body / Target criteria: correlation / Refinement space: REAL
Details: Protocol: rigid body. Subunits iteratively fit with Chimera
Input PDB model: 1RIB
Chain ID: A, B

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