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- PDB-1wth: Crystal structure of gp5-S351L mutant and gp27 complex -

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Basic information

Entry
Database: PDB / ID: 1wth
TitleCrystal structure of gp5-S351L mutant and gp27 complex
Components
  • Baseplate structural protein Gp27
  • Tail-associated lysozyme
KeywordsHydrolase/Structural protein / Triple-stranded beta-helix / OB fold / pseudohexamer / T4 tail lysozyme / HUB / gp5-gp27 / Hydrolase-Structural protein COMPLEX
Function / homology
Function and homology information


symbiont entry into host cell via disruption of host cell wall peptidoglycan / virus tail, baseplate / viral tail assembly / symbiont entry into host cell via disruption of host cell envelope / virus tail / symbiont entry into host / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity ...symbiont entry into host cell via disruption of host cell wall peptidoglycan / virus tail, baseplate / viral tail assembly / symbiont entry into host cell via disruption of host cell envelope / virus tail / symbiont entry into host / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to bacterium / symbiont entry into host cell / identical protein binding
Similarity search - Function
Bacteriophage T4, Gp27, baseplate hub, domain 3 / Nucleic acid-binding protein domain / Nuclear Transport Factor 2; Chain: A, - #190 / Phage tail proteins - 2 layer sandwich fold - #40 / Phage tail protein beta-alpha-beta fold - #20 / Bacteriophage T4, Gp27, baseplate hub, C-terminal / Bacteriophage T4, Gp27, baseplate hub, N-terminal / Gp27, baseplate hub, domain 3 / Gp27, baseplate hub, domain 4 / Gp27, baseplate hub, domain 2 ...Bacteriophage T4, Gp27, baseplate hub, domain 3 / Nucleic acid-binding protein domain / Nuclear Transport Factor 2; Chain: A, - #190 / Phage tail proteins - 2 layer sandwich fold - #40 / Phage tail protein beta-alpha-beta fold - #20 / Bacteriophage T4, Gp27, baseplate hub, C-terminal / Bacteriophage T4, Gp27, baseplate hub, N-terminal / Gp27, baseplate hub, domain 3 / Gp27, baseplate hub, domain 4 / Gp27, baseplate hub, domain 2 / Baseplate structural protein, domain 2 / Baseplate structural protein, domain 1 / Protein Gp5, N-terminal OB-fold domain / Gp5, C-terminal / Pre-baseplate central spike protein Gp5 / Gp5 N-terminal OB domain / Gp5 C-terminal repeat (3 copies) / Phage tail protein beta-alpha-beta fold / Phage tail proteins - 2 layer sandwich fold / 3-Layer(bab) Sandwich / Lysozyme - #40 / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / Elongation Factor Tu (Ef-tu); domain 3 / Nuclear Transport Factor 2; Chain: A, / Lysozyme / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Lysozyme-like domain superfamily / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Roll / Beta Barrel / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / PHOSPHATE ION / Pre-baseplate central spike protein Gp5 / Baseplate central spike complex protein gp27
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.8 Å
AuthorsKanamaru, S. / Ishiwata, Y. / Suzuki, T. / Rossmann, M.G. / Arisaka, F.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Control of bacteriophage t4 tail lysozyme activity during the infection process
Authors: Kanamaru, S. / Ishiwata, Y. / Suzuki, T. / Rossmann, M.G. / Arisaka, F.
History
DepositionNov 23, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 8, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tail-associated lysozyme
D: Baseplate structural protein Gp27
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,9054
Polymers108,7712
Non-polymers1342
Water5,008278
1
A: Tail-associated lysozyme
D: Baseplate structural protein Gp27
hetero molecules

A: Tail-associated lysozyme
D: Baseplate structural protein Gp27
hetero molecules

A: Tail-associated lysozyme
D: Baseplate structural protein Gp27
hetero molecules


Theoretical massNumber of molelcules
Total (without water)326,71512
Polymers326,3136
Non-polymers4026
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 area68590 Å2
ΔGint-316 kcal/mol
Surface area103210 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)137.134, 137.134, 396.042
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-585-

K

21A-586-

PO4

31A-586-

PO4

41A-639-

HOH

51A-717-

HOH

61A-718-

HOH

DetailsThe biological assembly is a hexamer generated from the two polypeptides in the asymmetric unit by the operations: -y,x-y,z and -x+y,-x,z

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Components

#1: Protein Tail-associated lysozyme / Protein Gp5


Mass: 64339.988 Da / Num. of mol.: 1 / Mutation: S351L
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: 5 / Plasmid: pET29a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P16009, lysozyme
#2: Protein Baseplate structural protein Gp27 / Hub protein 27


Mass: 44431.062 Da / Num. of mol.: 1
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: 27 / Plasmid: pET29a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P17172
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 278 / 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: 3.4 Å3/Da / Density % sol: 64 %
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 8000, Tris, Glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 279K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.0332 Å
DetectorType: SBC / Detector: CCD / Date: Nov 15, 2002
RadiationMonochromator: 1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.8→47.55 Å / Num. all: 35805 / Num. obs: 33875 / % possible obs: 94.7 % / Observed criterion σ(F): 0 / Biso Wilson estimate: 43 Å2
Reflection shellResolution: 2.8→2.93 Å / % possible all: 87.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MIR
Starting model: PDB ENTRY 1K28

1k28


Resolution: 2.8→47.55 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 542137.47 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.281 3393 10 %RANDOM
Rwork0.217 ---
obs0.217 33875 94.7 %-
all-35767 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.5663 Å2 / ksol: 0.314893 e/Å3
Displacement parametersBiso mean: 51.54 Å2
Baniso -1Baniso -2Baniso -3
1-12.44 Å217.77 Å20 Å2
2--12.44 Å20 Å2
3----24.87 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.59 Å0.44 Å
Refinement stepCycle: LAST / Resolution: 2.8→47.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7293 0 4 278 7575
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d25
X-RAY DIFFRACTIONc_improper_angle_d0.79
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection obs% reflection obs (%)
2.8-2.930.440910.30.3246170.02384787.3
2.93-3.080.3443810.2820.018393798.1
3.08-3.270.353970.2740.018411892.7
3.27-3.530.2894320.2360.014422195.5
3.53-3.880.2824560.2150.013430796.9
3.88-4.440.2544270.1850.012436097.6
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER_REP.TOP

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