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

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Basic information

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 Å resolution / Particle / Single particle)
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.

Validation Report
SummaryFull reportAbout validation report
DateDeposition: May 19, 2003 / Release: Sep 9, 2003
RevisionDateData content typeGroupProviderType
1.0Sep 9, 2003Structure modelrepositoryInitial release
1.1Apr 29, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance
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)537,40818
Polyers537,40818
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: 29856.020 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 experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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Sample preparation

Component
IDNameDetailsTypeParent ID
1T4 baseplate-tail tube complexT4 double mutant, 18-,23-, produces baseplate-tail tube assembliesVIRUS0
2gp12trimer1
Buffer solutionName: water / Details: water / pH: 7
SpecimenConc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: holey carbon
VitrificationCryogen name: ETHANE / Details: 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 / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 45000 / Calibrated magnification: 47000 / Nominal defocus max: 5000 nm / Nominal defocus min: 1200 nm / Cs: 2 mm
Specimen holderTemperature: 70 kelvins / Tilt angle max: 0 deg. / Tilt angle min: 0 deg.
Image recordingElectron dose: 25 e/Å2 / Film or detector model: KODAK SO-163 FILM

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Processing

EM software
IDNameVersionCategory
1SITUS COLORES2MODEL FITTING
2SPIDERRECONSTRUCTION
CTF correctionDetails: CTF correction of individual particles with Wiener filtering
SymmetryPoint symmetry: C6
3D reconstructionMethod: 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 buildingDetails: REFINEMENT PROTOCOL--Laplacian transform real space
Ref protocol: OTHER / 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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