EMDB-5432: dATP-inhibited class Ia ribonucleotide reductase from ...

Entry
Summary
Database / ID	EM DATA BANK (EMDB) / 5432
Authors	Zimanyi CM, Ando N, Brignole E, Asturias FJ, Stubbe J, Drennan CL
EMDB Sites	EMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
Movies	Movie Page #1: Surface view with section colored by density value, Surface level: 1.95, Made by UCSF CHIMERA #2: Surface view colored by cylindrical radius, Surface level: 1.95, Made by UCSF CHIMERA
Supplemental images	EMDB figure
Structure viewers	Yorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Related Entries	EMDB-5430 Cite EMDB-5431 Cite EMDB-5433 Cite EMDB-5434 Cite EMDB-5435 Cite EMDB-5436 Cite EMDB-5437 Cite PDB-4erm Cite PDB-4erp Cite Cite: data citing same article

Article
Citation - Primary
Article	Structure, Vol. 20, Issue 8, Page 1374-83, Year 2012
Title	Tangled up in knots: structures of inactivated forms of E. coli class Ia ribonucleotide reductase.
Authors	Christina M Zimanyi, Nozomi Ando, Edward J Brignole, Francisco J Asturias, Joanne Stubbe, Catherine L Drennan Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
Keywords	2'-deoxyadenosine triphosphate (1927-31-7), Crystallography, X-Ray, Cytidine Diphosphate (analogs & derivatives, 63-38-7), Deoxyadenine Nucleotides (chemistry), Escherichia coli Proteins (antagonists & inhibitors), Exoribonucleases (antagonists & inhibitors, 3.1.-), Microscopy, Electron, Models, Molecular, Protein Binding, Protein Structure, Quaternary, Protein Subunits (antagonists & inhibitors), Scattering, Small Angle, X-Ray Diffraction, gemcitabine-5'-diphosphate, rnr protein, E coli
Links	PII: S0969-2126(12)00211-0, DOI: 10.1016/j.str.2012.05.009, PubMed: 22727814, PMC: PMC3459064

File

Projections & Slices

Size of images:

Images are generated by Spider package.

(generated in cubic-lattice coordinate)

Density

Data Type

Image stored as Reals

Space Group Number

Map Geometry

Unit Cell

A = 313.92 A , B = 313.92 A , C = 470.88 A ,
alpha = 90.0 degrees , beta = 90.0 degrees , gamma = 90.0 degrees

Pixel Spacing

X = 4.36 A , Y = 4.36 A , Z = 6.54 A

CCP4 map header info

Annotation Details

alpha4beta4 open conformation 2

Sample
Name	E. coli Class Ia ribonucleotide reductase
Number of Components	1
Oligomeric State	two alpha2 subunits in complex with two beta2 subunits
Theoretical Mass	0.517 MDa
Mass-estimation Method	Calculated from amino acid sequence of subunits
Experimental Mass	0.517 MDa
Component #1: protein - RNR
Scientific name	E. coli Class Ia ribonucleotide reductase
Common Name	RNR
Theoretical Mass	0.517 MDa
Experimental Mass	0.517 MDa
Details	alpha4beta4 open conformation
Oligomeric Details	hetero-octamer
Number of Copies	1
Scientific Name of Species	Escherichia coli (NCBI Taxonomy: 562)
Recombinant expression	Yes
Engineered Source	Exp System: Escherichia coli (NCBI Taxonomy: 562)
Links	Gene Ontology: GO:0005971

Experiment
Sample Preparation
Staining	5ul protein, washed immediately 3x [2% uranyl acetate, 0.2% trehalose], carbon sandwich
Specimen Support Details	thin carbon support on 300 mesh Cu/Rh grid, glow discharge in amylamine
Specimen State	particle
Buffer	Details: 50 mM HEPES, 15 mM MgCl2, 1 mM EDTA, 1 mM CDP, 0.05 mM dATP pH: 7.6
Vitrification
Cryogen Name	NONE
Instrument	NONE
Imaging
Microscope	FEI TECNAI F20
Date	31-JUL-2010
Electron Gun
Electron Source	FIELD EMISSION GUN
Accelerating Voltage	120 kV
Electron Dose	25 e/A**2
Illumination Mode	FLOOD BEAM
Lens
Magnification	Nominal: 50000 X,
Nominal Cs	2.0 mm
Imaging Mode	BRIGHT FIELD
Defocus	275 nm - 1801 nm
Specimen Holder
Holder	room temperature ( SIDE ENTRY, EUCENTRIC )
Tilt Angle	-59.1 degrees - -54.3 degrees
Camera
Detector	Gatan Ultrascan 4000
Image Acquisition
Number of Digital Images	89
Quant Bit Number	16
Details	images acquired as tilt-pairs

Processing
Method	single particle reconstruction
3 D reconstruction
Algorithm	random conical tilt
Software	SPIDER
CTF Correction	each particle
Resolution By Author	32.1
Resolution Method	FSC at 0.5 cut-off
Single Particle
Number of Projections	452
Details	Semi-automated particle selection from untilted images with EMAN2. Particles matched in tilted images using modified TiltPicker. Processed in SPIDER.
Atomic Model Fitting
Model #0
Details	Protocol: rigid body. Subunits iteratively fit with Chimera
Refinement Protocol	rigid body
Refinement Space	REAL
Target Criteria	correlation
Software	Chimera
Model #1
Refinement Space	REAL
Target Criteria	correlation
Refinement Protocol	rigid body
Details	Protocol: rigid body. Subunits iteratively fit with Chimera
Software	Chimera

Data from EMDB

Header (meta data in XML format)

Map data

FTP directory

Movie files

movie #1

	.mp4 (H.264/MPEG-4 AVC format), 3.5 MB .webm (WebM/VP8 format), 5.4 MB Session file for UCSF-Chimera, 26.5 KB

movie #2

	.mp4 (H.264/MPEG-4 AVC format), 3.2 MB .webm (WebM/VP8 format), 4.9 MB Session file for UCSF-Chimera, 26.6 KB