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- PDB-2fkk: Crystal structure of the C-terminal domain of the bacteriophage T... -

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Basic information

Entry
Database: PDB / ID: 2fkk
TitleCrystal structure of the C-terminal domain of the bacteriophage T4 gene product 10
ComponentsBaseplate structural protein Gp10
KeywordsVIRAL PROTEIN / Bacteriophage T4 / Baseplate / Tail / Evolution / gp10 / Structural comparisons
Function / homology
Function and homology information


virus tail, baseplate / viral tail assembly / viral release from host cell
Similarity search - Function
Baseplate wedge protein gp10 / Baseplate structural protein Gp9/Gp10 / Baseplate structural protein Gp9/Gp10 middle domain superfamily / Gp9-like superfamily / Bacteriophage T4 gp9/10-like protein
Similarity search - Domain/homology
BROMIDE ION / PHOSPHITE ION / Baseplate wedge protein gp10
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.2 Å
AuthorsLeiman, P.G. / Shneider, M.M. / Mesyanzhinov, V.V. / Rossmann, M.G.
CitationJournal: J Mol Biol / Year: 2006
Title: Evolution of bacteriophage tails: Structure of T4 gene product 10.
Authors: Petr G Leiman / Mikhail M Shneider / Vadim V Mesyanzhinov / Michael G Rossmann /
Abstract: The success of tailed bacteriophages to infect cells far exceeds that of most other viruses on account of their specialized tail and associated baseplate structures. The baseplate protein gene ...The success of tailed bacteriophages to infect cells far exceeds that of most other viruses on account of their specialized tail and associated baseplate structures. The baseplate protein gene product (gp) 10 of bacteriophage T4, whose structure was determined to 1.2 A resolution, was fitted into the cryo-electron microscopy structures of the pre and post-infection conformations of the virus. gp10 functions as a molecular lever that rotates and extends the hinged short tail fibers to facilitate cell attachment. The central folding motif of the gp10 trimer is similar to that of the baseplate protein gp11 and to the receptor-binding domain of the short tail fiber, gp12. The three proteins comprise the periphery of the baseplate and interact with each other. The structural and functional similarities of gp10, gp11, and gp12 and their sequential order in the T4 genome suggest that they evolved separately, subsequent to gene triplication from a common ancestor. Such events are usual in the evolution of complex organelles from a common primordial molecule.
History
DepositionJan 4, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Baseplate structural protein Gp10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9628
Polymers22,4321
Non-polymers5297
Water6,539363
1
A: Baseplate structural protein Gp10
hetero molecules

A: Baseplate structural protein Gp10
hetero molecules

A: Baseplate structural protein Gp10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,88524
Polymers67,2973
Non-polymers1,58821
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area26640 Å2
ΔGint-94 kcal/mol
Surface area22860 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)69.843, 69.843, 119.672
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-701-

BR

21A-710-

PO3

31A-801-

TRS

41A-801-

TRS

51A-1016-

HOH

61A-1020-

HOH

71A-1048-

HOH

81A-1049-

HOH

91A-1050-

HOH

101A-1054-

HOH

111A-1213-

HOH

DetailsThe biological assembly is a trimer. The second and third chains can be generated by using the symmetry operators of the crystallographic threefold axis: -y+1, x-y, z and y-x+1, -x+1, z

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Baseplate structural protein Gp10 / Baseplate wedge protein 10


Mass: 22432.246 Da / Num. of mol.: 1 / Fragment: C-terminal domain / Mutation: A442E, A530T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Genus: T4-like viruses / Species: Enterobacteria phage T4 sensu lato / Strain: D / Gene: 10 / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21/DE3 / References: UniProt: P10928

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Non-polymers , 5 types, 370 molecules

#2: Chemical ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#3: Chemical ChemComp-PO3 / PHOSPHITE ION / Phosphite ester


Mass: 78.972 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO3
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 363 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.75 Å3/Da / Density % sol: 67.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 2.3
Details: 6% PEG1000, 8% PEG8000, 100 mM glycine-HCl pH 2.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 25, 2005
Details: Bent conical Si-mirror (Rh coated), Bent Ge(111) monochromator
RadiationMonochromator: Bent conical Si-mirror (Rh coated), Bent Ge(111) monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.2→30 Å / Num. all: 106155 / Num. obs: 105624 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.4 % / Biso Wilson estimate: 18.2 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Net I/σ(I): 20.8
Reflection shellResolution: 1.2→1.22 Å / Redundancy: 5 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2.5 / Num. unique all: 5221 / Rsym value: 0.39 / % possible all: 99.7

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
SHELXL-97refinement
RefinementMethod to determine structure: AB INITIO PHASING
Starting model: none

Resolution: 1.2→10 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1364 2633 -RANDOM
Rwork0.119 ---
all0.12 105438 --
obs0.12 105438 97.1 %-
Refinement stepCycle: LAST / Resolution: 1.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1419 0 29 363 1811
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d0.034
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.085
X-RAY DIFFRACTIONs_approx_iso_adps0.128
X-RAY DIFFRACTIONs_bond_d0.016
X-RAY DIFFRACTIONs_from_restr_planes0.0317

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