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- PDB-1pdi: Fitting of the C-terminal part of the short tail fibers into the ... -

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Entry
Database: PDB / ID: 1pdi
TitleFitting of the C-terminal part of the short tail fibers into the cryo-EM reconstruction of T4 baseplate
DescriptorShort tail fiber protein
KeywordsSTRUCTURAL PROTEIN
Specimen sourceEnterobacteria phage T4 / virus
MethodElectron microscopy (12 A resolution / Single particle / Vitreous ice (cryo EM))
AuthorsKostyuchenko, V.A. / Leiman, P.G. / Chipman, P.R. / Kanamaru, S. / van Raaij, M.J. / Arisaka, F. / Mesyanzhinov, V.V. / Rossmann, M.G.
CitationNat. Struct. Biol., 2003, 10, 688-693

primary. Nat. Struct. Biol., 2003, 10, 688-693 StrPapers
Three-dimensional structure of bacteriophage T4 baseplate.
Victor A Kostyuchenko / Petr G Leiman / Paul R Chipman / Shuji Kanamaru / Mark J van Raaij / Fumio Arisaka / Vadim V Mesyanzhinov / Michael G Rossmann

#1. J.Mol.Biol., 2001, 314, 1137-1146
Crystal Structure of a Heat-and Protease-Stable Part of the Bacteriophage T4 Short Tail Fibre
van Raaij, M.J. / Schoehn, G. / Burda, M.R. / Miller, S.

#2. To be published Search PubMed
Structure of the receptor-binding domain of the bacteriophage T4 short tail fibre
Thomassen, E. / Gielen, G. / Schuetz, M. / Miller, S. / van Raaij, M.J.

DateDeposition: May 19, 2003 / Release: Sep 9, 2003 / Last modification: Feb 24, 2009
Remark 999SEQUENCE 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 300BIOMOLECULE: 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

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Assembly

Deposited unit
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


Theoretical massNumber of molelcules
Total (without water)537,41218
Polyers537,41218
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Polypeptide(L)
Short tail fiber protein / Protein Gp12 / p12


Mass: 29856.234 Da / Num. of mol.: 18 / Source: (natural) Enterobacteria phage T4 / virus / References: UniProt: P10930

Cellular component

Molecular function

Biological process

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentReconstruction method: SINGLE PARTICLE / Specimen type: VITREOUS ICE (CRYO EM)

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Sample preparation

Assembly of specimenName: T4 baseplate-tail tube complex / Aggregation state: PARTICLE
Details: T4 double mutant, 18-,23-, produces baseplate-tail tube assemblies
ComponentName: gp12 / Details: trimer
Buffer solutionName: water
Sample preparationpH: 7 / Sample conc.: 5 mg/ml
Specimen supportDetails: holey carbon
VitrificationDetails: ethane vitrification
Crystal grow
*PLUS
Temp unit: K / Method: electron microscopy

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Electron microscopy imaging

MicroscopyMicroscope model: FEI/PHILIPS CM300FEG/T / Date: Jan 30, 2001
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 25 e/A2 / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 45000 X / Calibrated magnification: 47000 X / Nominal defocus max: 5000 nm / Nominal defocus min: 1200 nm / Cs: 2 mm
Specimen holderTemperature: 70 K / Tilt angle max: 0 deg. / Tilt angle min: 0 deg.
CameraType: KODAK SO163 FILM

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Processing

Image selectionSoftware name: situs 2.0/colores / Number of particles: 945
EM single particle entitySymmetry type: CYCLIC
3D reconstructionMethod: model-based projection matching / Resolution: 12 A / Nominal pixel size: 3.11 A/pix / Actual pixel size: 2.98 A/pix / Magnification calibration: TMV particles images
CTF correction method: CTF correction of individual particles with Wiener filtering
Details: modifed version of program SPIDER was used for the reconstruction
Atomic model buildingSoftware name: situs 2.0/colores / Ref protocol: Laplacian transform real space / Ref space: REAL / Target criteria: Correlation Coefficient maximization
Atomic model buildingPDB-ID: 1OCY
Number of atoms included #LASTProtein: 5004 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 5004

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