|Entry||Database: PDB / ID: 1pdi|
|Title||Fitting of the C-terminal part of the short tail fibers into the cryo-EM reconstruction of T4 baseplate|
|Descriptor||Short tail fiber protein|
|Specimen source||Enterobacteria phage T4 / virus|
|Method||Electron microscopy (12 Å resolution / Particle / Single particle)|
|Authors||Kostyuchenko, V.A. / Leiman, P.G. / Chipman, P.R. / Kanamaru, S. / van Raaij, M.J. / Arisaka, F. / Mesyanzhinov, V.V. / Rossmann, M.G.|
|Citation||Nat. Struct. Biol., 2003, 10, 688-693|
primary. Nat. Struct. Biol., 2003, 10, 688-693 Yorodumi Papers
#1. J.Mol.Biol., 2001, 314, 1137-1146
SummaryFull reportAbout validation report
|Date||Deposition: May 19, 2003 / Release: Sep 9, 2003|
|Remark 999||SEQUENCE The differences between the database reference sequence and the deposited sequence arise because the source of the fitted model is bacteriophage T4alc7, whereas the protein used in the structural solution is from bacteriophage T4D. The sequence of the protein from T4D has not yet been deposited. Only coordinates for CA atoms were submitted.|
|Remark 300||BIOMOLECULE: 1 THIS ENTRY CONTAINS A PORTION OF THE BIOLOGICALLY SIGNIFICANT MULTIMER. ASSEMBLY COMPONENTS COM_ID: 1 NAME:GP12 IPR_ID: NULL GO_ID: NULL OTHER_DETAILS: TRIMER|
Downloads & links
A: Short tail fiber protein
B: Short tail fiber protein
C: Short tail fiber protein
D: Short tail fiber protein
E: Short tail fiber protein
F: Short tail fiber protein
G: Short tail fiber protein
H: Short tail fiber protein
I: Short tail fiber protein
J: Short tail fiber protein
K: Short tail fiber protein
L: Short tail fiber protein
M: Short tail fiber protein
N: Short tail fiber protein
O: Short tail fiber protein
P: Short tail fiber protein
Q: Short tail fiber protein
R: Short tail fiber protein
Mass: 29856.020 Da / Num. of mol.: 18 / Source: (natural) Enterobacteria phage T4 / virus / References: UniProt: P10930
|Experiment||Method: ELECTRON MICROSCOPY|
|EM experiment||Aggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE|
|Buffer solution||Name: water / Details: water / pH: 7|
|Specimen||Conc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES|
|Specimen support||Details: holey carbon|
|Vitrification||Cryogen name: ETHANE / Details: ethane vitrification|
*PLUSTemp unit: K / Method: electron microscopy
-Electron microscopy imaging
|Microscopy||Microscope model: FEI/PHILIPS CM300FEG/T / Date: Jan 30, 2001|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM|
|Electron lens||Mode: BRIGHT FIELD / Nominal magnification: 45000 / Calibrated magnification: 47000 / Nominal defocus max: 5000 nm / Nominal defocus min: 1200 nm / Cs: 2 mm|
|Specimen holder||Temperature: 70 kelvins / Tilt angle max: 0 deg. / Tilt angle min: 0 deg.|
|Image recording||Electron dose: 25 e/Å2 / Film or detector model: KODAK SO-163 FILM|
|CTF correction||Details: CTF correction of individual particles with Wiener filtering|
|Symmetry||Point symmetry: C6|
|3D reconstruction||Method: model-based projection matching / Resolution: 12 Å / Number of particles: 945 / Nominal pixel size: 3.11 / Actual pixel size: 2.98 / Magnification calibration: TMV particles images|
Details: modifed version of program SPIDER was used for the reconstruction
Symmetry type: POINT
|Atomic model building||Details: REFINEMENT PROTOCOL--Laplacian transform real space|
Ref protocol: OTHER / Ref space: REAL / Target criteria: Correlation Coefficient maximization
|Atomic model building||PDB-ID: 1OCY|
|Number of atoms included #LAST||Protein: 5004 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 5004|
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