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- PDB-3h2t: Crystal structure of gene product 6, baseplate protein of bacteri... -

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Basic information

Entry
Database: PDB / ID: 3h2t
TitleCrystal structure of gene product 6, baseplate protein of bacteriophage T4
ComponentsBaseplate structural protein Gp6
KeywordsVIRAL PROTEIN / Virion
Function / homology
Function and homology information


virus tail, baseplate / viral tail assembly / identical protein binding
Similarity search - Function
GMP Synthetase; Chain A, domain 3 - #200 / Baseplate wedge protein gp6 / : / : / : / : / Baseplate wedge protein gp6-like, helical domain / Baseplate structural protein gp6, C-terminal domain I / Baseplate structural protein gp6, C-terminal domain II / Baseplate wedge protein gp6, domain II ...GMP Synthetase; Chain A, domain 3 - #200 / Baseplate wedge protein gp6 / : / : / : / : / Baseplate wedge protein gp6-like, helical domain / Baseplate structural protein gp6, C-terminal domain I / Baseplate structural protein gp6, C-terminal domain II / Baseplate wedge protein gp6, domain II / GMP Synthetase; Chain A, domain 3 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Baseplate wedge protein gp6
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.2 Å
AuthorsAksyuk, A.A. / Leiman, P.G. / Shneider, M.M. / Mesyanzhinov, V.V. / Rossmann, M.G.
CitationJournal: Structure / Year: 2009
Title: The structure of gene product 6 of bacteriophage T4, the hinge-pin of the baseplate.
Authors: Anastasia A Aksyuk / Petr G Leiman / Mikhail M Shneider / Vadim V Mesyanzhinov / Michael G Rossmann /
Abstract: The baseplate of bacteriophage T4 is a multicomponent protein complex, which controls phage attachment to the host. It assembles from six wedges and a central hub. During infection the baseplate ...The baseplate of bacteriophage T4 is a multicomponent protein complex, which controls phage attachment to the host. It assembles from six wedges and a central hub. During infection the baseplate undergoes a large conformational change from a dome-shaped to a flat, star-shaped structure. We report the crystal structure of the C-terminal half of gene product (gp) 6 and investigate its motion with respect to the other proteins during the baseplate rearrangement. Six gp6 dimers interdigitate, forming a ring that maintains the integrity of the baseplate in both conformations. One baseplate wedge contains an N-terminal dimer of gp6, whereas neighboring wedges are tied together through the C-terminal dimer of gp6. The dimeric interactions are preserved throughout the rearrangement of the baseplate. However, the hinge angle between the N- and C-terminal parts of gp6 changes by approximately 15 degrees , accounting for a 10 A radial increase in the diameter of the gp6 ring.
History
DepositionApr 14, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 19, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 20, 2013Group: Other
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Baseplate structural protein Gp6
B: Baseplate structural protein Gp6


Theoretical massNumber of molelcules
Total (without water)76,6092
Polymers76,6092
Non-polymers00
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-9.9 kcal/mol
Surface area32140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.774, 94.579, 136.221
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsSIX DIMERS FORM A RING IN THE BACTERIOPHAGE T4 BASEPLATE

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Components

#1: Protein Baseplate structural protein Gp6 / Baseplate wedge protein 6


Mass: 38304.449 Da / Num. of mol.: 2 / Fragment: UNP residues 334-660
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Strain: D / Gene: 6, gene 6 / Plasmid: pET22 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P19060
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.23 Å3/Da / Density % sol: 61.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7
Details: 1.2 M Ammonium Sulfate, buffered with HEPES, pH 7.0, VAPOR DIFFUSION, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 23-ID-D10.97948
SYNCHROTRONAPS 23-ID-D20.97948
Detector
TypeIDDetectorDate
MARMOSAIC 300 mm CCD1CCDJun 2, 2008
MARMOSAIC 300 mm CCD2CCDFeb 14, 2007
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Double crystal cryo-cooled Si(111)SADMx-ray1
2Double crystal cryo-cooled Si(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 0.97948 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. all: 16941 / Num. obs: 16878 / % possible obs: 99.63 % / Observed criterion σ(I): 2 / Redundancy: 7.2 % / Biso Wilson estimate: 80.95 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 26.9
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.476 / Mean I/σ(I) obs: 3.9 / % possible all: 97

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Processing

Software
NameClassification
HKL-2000data collection
SHELXCDphasing
SHELXEmodel building
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 3.2→44.856 Å / SU ML: 0.82 / Cross valid method: THROUGHOUT / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.3216 863 5.11 %random
Rwork0.2297 ---
obs0.2344 16878 99.63 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 74.61 Å2 / ksol: 0.337 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-22.7658 Å20 Å20 Å2
2---9.6198 Å2-0 Å2
3----13.146 Å2
Refinement stepCycle: LAST / Resolution: 3.2→44.856 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5230 0 0 19 5249
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075334
X-RAY DIFFRACTIONf_bond_d_na
X-RAY DIFFRACTIONf_bond_d_prot
X-RAY DIFFRACTIONf_angle_d1.2157242
X-RAY DIFFRACTIONf_angle_d_na
X-RAY DIFFRACTIONf_angle_d_prot
X-RAY DIFFRACTIONf_angle_deg
X-RAY DIFFRACTIONf_angle_deg_na
X-RAY DIFFRACTIONf_angle_deg_prot
X-RAY DIFFRACTIONf_dihedral_angle_d19.1461927
X-RAY DIFFRACTIONf_dihedral_angle_d_na
X-RAY DIFFRACTIONf_dihedral_angle_d_prot
X-RAY DIFFRACTIONf_improper_angle_d0.087813
X-RAY DIFFRACTIONf_improper_angle_d_na
X-RAY DIFFRACTIONf_improper_angle_d_prot
X-RAY DIFFRACTIONf_mcbond_it
X-RAY DIFFRACTIONf_mcangle_it
X-RAY DIFFRACTIONf_scbond_it
X-RAY DIFFRACTIONf_scangle_it
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.2-3.40040.39421330.2705260199
3.4004-3.66290.36341450.23942621100
3.6629-4.03130.31611530.22022623100
4.0313-4.61410.26321430.1922652100
4.6141-5.81130.28211430.19972698100
5.8113-44.860.30941460.22372820100

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