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- PDB-1pdj: Fitting of gp27 into cryoEM reconstruction of bacteriophage T4 ba... -

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Entry
Database: PDB / ID: 1pdj
TitleFitting of gp27 into cryoEM reconstruction of bacteriophage T4 baseplate
DescriptorBaseplate structural protein Gp27
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. Nature, 2002, 415, 553-557
Structure of the cell-puncturing device of bacteriophage T4
Kanamaru, S. / Leiman, P.G. / Kostyuchenko, V.A. / Chipman, P.R. / Mesyanzhinov, V.V. / Arisaka, F. / Rossmann, M.G.

DateDeposition: May 19, 2003 / Release: Sep 9, 2003 / Last modification: Feb 24, 2009
Remark 999SEQUENCE ONLY COORDINTES FOR CA ATOMS SUBMITTED.
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS A PORTION OF THE BIOLOGICALLY SIGNIFICANT MULTIMER. ASSEMBLY COMPONENTS COM_ID: 1 NAME:GP27 IPR_ID: NULL GO_ID: NULL OTHER_DETAILS: TRIMER

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Assembly

Deposited unit
D: Baseplate structural protein Gp27
E: Baseplate structural protein Gp27
F: Baseplate structural protein Gp27


Theoretical massNumber of molelcules
Total (without water)133,2943
Polyers133,2943
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Polypeptide(L)Baseplate structural protein Gp27 / Hub protein 27


Mass: 44431.465 Da / Num. of mol.: 3 / Source: (natural) Enterobacteria phage T4 / virus / References: UniProt: P17172

Cellular component

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
ComponentName: gp27 / Details: trimer
Buffer solutionName: water
Sample preparationpH: 7 / Sample conc.: 5
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 / Electron dose: 25 / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 45000 / Calibrated magnification: 47000 / Nominal defocus max: 5000 / Nominal defocus min: 1200 / Cs: 2
Specimen holderTemperature: 70 / Tilt angle max: 0 / Tilt angle min: 0
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 / Nominal pixel size: 3.11 / Actual pixel size: 2.98 / Magnification calibration: TMV images
CTF correction method: CTF was corrected for each particle with Wiener filtering
Details: a modified version of SPIDER was used for the reconstruction
Atomic model buildingSoftware name: situs 2.0/colores / Ref protocol: laplacian filtered real space / Ref space: REAL / Target criteria: Correlation coefficient maximization
Atomic model buildingPDB-ID: 1K28
Number of atoms included #LASTProtein: 1092 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 1092

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