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- EMDB-1135: Quaternary polymorphism of replicative helicase G40P: structural ... -

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Basic information

Entry
Database: EMDB / ID: 1135
TitleQuaternary polymorphism of replicative helicase G40P: structural mapping and domain rearrangement.
Map dataBacteriophage SPP1 helicase G40P: C6 architecture
SampleC6 architecture of Bacteriophage SPP1 replicative helicase G40P:
helicase
SourceBacillus phage SPP1 (bacteriophage)
Methodsingle particle reconstruction / negative staining / 24 Å resolution
AuthorsNunez-Ramirez R / Robledo Y / mesa P / Alonso JC / Carazo JM / Donate LE
CitationJournal: J. Mol. Biol. / Year: 2006
Title: Quaternary polymorphism of replicative helicase G40P: structural mapping and domain rearrangement.
Authors: Rafael Núñez-Ramírez / Yolanda Robledo / Pablo Mesa / Silvia Ayora / Juan Carlos Alonso / José María Carazo / Luis Enrique Donate
DateDeposition: Jul 13, 2005 / Header (metadata) release: Jul 14, 2005 / Map release: May 16, 2006 / Last update: Oct 24, 2012

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0053
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0053
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_1135.map.gz (map file in CCP4 format, 2001 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
80 pix
4.1 Å/pix.
= 328. Å
80 pix
4.1 Å/pix.
= 328. Å
80 pix
4.1 Å/pix.
= 328. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.1 Å
Density
Contour Level:0.00292, 0.0053 (movie #1):
Minimum - Maximum-0.0147015 - 0.0285048
Average (Standard dev.)0.000101116 (0.0014075)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions808080
Origin000
Limit797979
Spacing808080
CellA=B=C: 328 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.14.14.1
M x/y/z808080
origin x/y/z0.0000.0000.000
length x/y/z328.000328.000328.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-90-90-190
NX/NY/NZ180180380
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS808080
D min/max/mean-0.0150.0290.000

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Supplemental data

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Sample components

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Entire C6 architecture of Bacteriophage SPP1 replicative helicase G40P

EntireName: C6 architecture of Bacteriophage SPP1 replicative helicase G40P
Oligomeric State: Homohexamer / Number of components: 1
MassTheoretical: 300 kDa / Experimental: 300 kDa / Measured by: gel filtration chromatography

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Component #1: protein, helicase

ProteinName: helicase / Oligomeric Details: Hexamer / Recombinant expression: Yes / Number of Copies: 6
MassTheoretical: 300 kDa / Experimental: 300 kDa
SourceSpecies: Bacillus phage SPP1 (bacteriophage) / Strain: SPP1
Source (engineered)Expression System: Escherichia coli (E. coli) / Vector: pCB506
Source (natural)Cell: Bacteria

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: negative staining
Sample solutionSpecimen conc.: 0.2 mg/ml
Buffer solution: 50mM HEPES, 50mM NaCl, 10mM MgCl2, 1mM ATP, 1mM dithithreitol
pH: 7
Support filmcollodion/carbon coated 400 mesh copper grid
StainingGrids with adsorbed protein satined on 2% uranyl acetate for 1 minute
VitrificationCryogen name: NONE

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Electron microscopy imaging

ImagingMicroscope: JEOL 2000EX
Electron gunElectron source: TUNGSTEN HAIRPIN / Accelerating voltage: 80 kV / Electron dose: 20 e/Å2 / Illumination mode: OTHER
LensMagnification: 60000 X (nominal) / Imaging mode: OTHER
Specimen HolderHolder: Eucentric / Model: OTHER
CameraDetector: KODAK SO-163 FILM

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Image acquisition

Image acquisitionNumber of digital images: 40 / Scanner: ZEISS SCAI / Sampling size: 21 microns / Bit depth: 8

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 700 / Applied symmetry: C6 (6 fold cyclic)
3D reconstructionAlgorithm: Random Conical / Software: SPIDER Xmipp / Resolution: 24 Å / Resolution method: FSC 0.5

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