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- PDB-1qex: BACTERIOPHAGE T4 GENE PRODUCT 9 (GP9), THE TRIGGER OF TAIL CONTRA... -

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Basic information

Entry
Database: PDB / ID: 1qex
TitleBACTERIOPHAGE T4 GENE PRODUCT 9 (GP9), THE TRIGGER OF TAIL CONTRACTION AND THE LONG TAIL FIBERS CONNECTOR
ComponentsPROTEIN (BACTERIOPHAGE T4 GENE PRODUCT 9 (GP9))
KeywordsVIRAL PROTEIN / BACTERIOPHAGE T4 / BASEPLATE / GENE PRODUCT 9 / OLIGOMERIZATION
Function / homology
Function and homology information


virus tail, baseplate / viral tail assembly / viral release from host cell
Similarity search - Function
Bacteriophage t4 gene product 9 (gp9) / gp9 / 4-oxalocrotonate tautomerase-like / Baseplate structural protein Gp9 C-terminal domain superfamily / Baseplate structural protein Gp9/Gp10 / Baseplate structural protein Gp9/Gp10 middle domain superfamily / Gp9-like superfamily / Bacteriophage T4 gp9/10-like protein / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Jelly Rolls ...Bacteriophage t4 gene product 9 (gp9) / gp9 / 4-oxalocrotonate tautomerase-like / Baseplate structural protein Gp9 C-terminal domain superfamily / Baseplate structural protein Gp9/Gp10 / Baseplate structural protein Gp9/Gp10 middle domain superfamily / Gp9-like superfamily / Bacteriophage T4 gp9/10-like protein / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Jelly Rolls / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Baseplate protein gp9
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / MIRAS / Resolution: 2.3 Å
AuthorsKostyuchenko, V.A. / Navruzbekov, G.A. / Kurochkina, L.P. / Strelkov, S.V. / Mesyanzhinov, V.V. / Rossmann, M.G.
Citation
Journal: Structure Fold.Des. / Year: 1999
Title: The structure of bacteriophage T4 gene product 9: the trigger for tail contraction.
Authors: Kostyuchenko, V.A. / Navruzbekov, G.A. / Kurochkina, L.P. / Strelkov, S.V. / Mesyanzhinov, V.V. / Rossmann, M.G.
#1: Journal: J.Mol.Biol. / Year: 1993
Title: Crystallization and preliminary crystallographic characterization of bacteriophage T4 baseplate protein encoded by gene 9.
Authors: Strelkov, S.V. / Zurabishvili, T.G. / Nepluev, I.V. / Efimov, V.P. / Isupov, M.N. / Harutyunyan, E.H. / Mesyanzhinov, V.V.
History
DepositionMar 30, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Oct 5, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Nov 20, 2019Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (BACTERIOPHAGE T4 GENE PRODUCT 9 (GP9))
B: PROTEIN (BACTERIOPHAGE T4 GENE PRODUCT 9 (GP9))
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,5264
Polymers62,0492
Non-polymers4772
Water5,260292
1
A: PROTEIN (BACTERIOPHAGE T4 GENE PRODUCT 9 (GP9))
B: PROTEIN (BACTERIOPHAGE T4 GENE PRODUCT 9 (GP9))
hetero molecules

A: PROTEIN (BACTERIOPHAGE T4 GENE PRODUCT 9 (GP9))
B: PROTEIN (BACTERIOPHAGE T4 GENE PRODUCT 9 (GP9))
hetero molecules

A: PROTEIN (BACTERIOPHAGE T4 GENE PRODUCT 9 (GP9))
B: PROTEIN (BACTERIOPHAGE T4 GENE PRODUCT 9 (GP9))
hetero molecules


Theoretical massNumber of molelcules
Total (without water)187,57812
Polymers186,1486
Non-polymers1,4306
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area44770 Å2
ΔGint-239 kcal/mol
Surface area65280 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)94.330, 94.330, 440.940
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.49937, 0.86639, 0.00032), (0.86639, 0.49937, -0.00029), (-0.00041, 0.00013, -1)
Vector: 0.02251, -0.00543, 195.82069)

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Components

#1: Protein PROTEIN (BACTERIOPHAGE T4 GENE PRODUCT 9 (GP9))


Mass: 31024.725 Da / Num. of mol.: 2
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 / Gene: 9 / Plasmid: PET-23D / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P10927
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 292 / 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: 3.1 Å3/Da / Density % sol: 60 %
Crystal growpH: 7.5 / Details: 28% PEG-400 0.2M CACL2 HEPES-NA BUFFER, PH 7.5
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
228 %(v/v)PEG4001reservoir
30.2 M1reservoirCaCl2
40.1 Msodium HEPES1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jun 1, 1997 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. obs: 33400 / % possible obs: 97.5 % / Observed criterion σ(I): -2 / Redundancy: 5.8 % / Biso Wilson estimate: 31.7 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 15
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 5 / % possible all: 96.3
Reflection shell
*PLUS
% possible obs: 96.3 %

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Processing

Software
NameVersionClassification
CCP4model building
CNS0.5refinement
DENZOdata reduction
SnBphasing
CCP4phasing
RefinementMethod to determine structure: MIRAS / Resolution: 2.3→20 Å / Rfactor Rfree error: 0.007 / Data cutoff high rms absF: 5466890.49 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 2
Details: DISORDERED REGIONS WERE MODELLED STEREOCHEMICALLY AND MARKED BY HIGH B-FACTORS
RfactorNum. reflection% reflectionSelection details
Rfree0.277 1637 4.9 %RANDOM
Rwork0.239 ---
obs-33400 97.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 36.78 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso mean: 34.5 Å2
Baniso -1Baniso -2Baniso -3
1-2.86 Å22.29 Å20 Å2
2--2.86 Å20 Å2
3----5.72 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.32 Å
Luzzati d res low-20 Å
Luzzati sigma a0.25 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4350 0 30 292 4672
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.86
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.271.5
X-RAY DIFFRACTIONc_mcangle_it2.222
X-RAY DIFFRACTIONc_scbond_it1.672
X-RAY DIFFRACTIONc_scangle_it2.432.5
LS refinement shellResolution: 2.3→2.4 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.304 223 5.5 %
Rwork0.28 3853 -
obs--96.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3HEPES.PARAMHEPES.TOP
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 2 / % reflection Rfree: 4.9 % / Rfactor obs: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 34.5 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.86
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Highest resolution: 2.3 Å / Rfactor Rfree: 0.304 / % reflection Rfree: 5.5 % / Rfactor Rwork: 0.28

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