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- PDB-7cn7: T4 phage spackle protein gp61.3 complex with lysozyme domain of g... -

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Basic information

Entry
Database: PDB / ID: 7cn7
TitleT4 phage spackle protein gp61.3 complex with lysozyme domain of gp5 tail lysozyme
Components
  • Baseplate central spike complex protein gp5
  • Protein spackle
KeywordsVIRAL PROTEIN / Lysozyme inhibitor complex / Phage / Lysis inhibition
Function / homology
Function and homology information


superinfection exclusion / host cell periplasmic space / symbiont entry into host cell via disruption of host cell wall peptidoglycan / virus tail, baseplate / symbiont entry into host cell via disruption of host cell envelope / viral tail assembly / virus tail / symbiont entry into host / peptidoglycan catabolic process / cell wall macromolecule catabolic process ...superinfection exclusion / host cell periplasmic space / symbiont entry into host cell via disruption of host cell wall peptidoglycan / virus tail, baseplate / symbiont entry into host cell via disruption of host cell envelope / viral tail assembly / 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
Protein spackle / Gp5, C-terminal / Gp5 C-terminal repeat (3 copies) / Protein Gp5, N-terminal OB-fold domain / Pre-baseplate central spike protein Gp5 / Gp5 N-terminal OB domain / Lysozyme - #40 / T4-type lysozyme / : / Glycoside hydrolase, family 24 ...Protein spackle / Gp5, C-terminal / Gp5 C-terminal repeat (3 copies) / Protein Gp5, N-terminal OB-fold domain / Pre-baseplate central spike protein Gp5 / Gp5 N-terminal OB domain / Lysozyme - #40 / T4-type lysozyme / : / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme domain superfamily / Lysozyme / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-1PG / Pre-baseplate central spike protein Gp5 / Protein spackle
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å
AuthorsKanamaru, S. / Leiman, P.G.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)23121538 Japan
Japan Society for the Promotion of Science (JSPS)18H05421 Japan
CitationJournal: Viruses / Year: 2020
Title: Structure and Function of the T4 Spackle Protein Gp61.3.
Authors: Kanamaru, S. / Uchida, K. / Nemoto, M. / Fraser, A. / Arisaka, F. / Leiman, P.G.
History
DepositionJul 30, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Baseplate central spike complex protein gp5
C: Protein spackle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,64711
Polymers29,0422
Non-polymers6059
Water6,756375
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3040 Å2
ΔGint-25 kcal/mol
Surface area12780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.720, 69.180, 83.820
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 2 types, 2 molecules AC

#1: Protein Baseplate central spike complex protein gp5 / Peptidoglycan hydrolase gp5 / Protein Gp5


Mass: 20353.336 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: SF file contains Friedel pairs. / Source: (gene. exp.) Enterobacteria phage T4 (virus) / Plasmid: pUC19 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P16009, lysozyme
#2: Protein Protein spackle


Mass: 8688.785 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Gene: sp, 61.3 / Plasmid: pUC19 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P39230

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Non-polymers , 5 types, 384 molecules

#3: Chemical ChemComp-1PG / 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL


Mass: 252.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H24O6
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 375 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: 2.33 Å3/Da / Density % sol: 47.26 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.4 / Details: PEG550MME, MES, KSCN

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 3, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.15→46.72 Å / Num. obs: 187608 / % possible obs: 99.8 % / Redundancy: 7.1 % / Biso Wilson estimate: 10.29 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.018 / Rrim(I) all: 0.047 / Χ2: 1.01 / Net I/σ(I): 24.5
Reflection shellResolution: 1.15→1.17 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.542 / Mean I/σ(I) obs: 0.859 / Num. unique obs: 4655 / CC1/2: 0.859 / Rpim(I) all: 0.23 / Rrim(I) all: 0.59 / Χ2: 1.01 / % possible all: 97.6

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Processing

Software
NameVersionClassification
PHENIX1.18_3845refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1k28

1k28


Resolution: 1.15→17.92 Å / SU ML: 0.0849 / Cross valid method: FREE R-VALUE / σ(F): 1 / Phase error: 10.4462
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1215 9381 5 %
Rwork0.1073 178227 -
obs0.1081 187608 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.28 Å2
Refinement stepCycle: LAST / Resolution: 1.15→17.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2004 0 37 375 2416
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00812296
X-RAY DIFFRACTIONf_angle_d1.06623105
X-RAY DIFFRACTIONf_chiral_restr0.077332
X-RAY DIFFRACTIONf_plane_restr0.0065406
X-RAY DIFFRACTIONf_dihedral_angle_d5.9634357
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.15-1.160.22332750.2275806X-RAY DIFFRACTION96.25
1.16-1.170.20142780.20315942X-RAY DIFFRACTION100
1.17-1.190.19282950.18435936X-RAY DIFFRACTION100
1.19-1.20.20943110.17545958X-RAY DIFFRACTION100
1.2-1.220.17033140.15865956X-RAY DIFFRACTION100
1.22-1.240.16453230.1486003X-RAY DIFFRACTION100
1.24-1.250.15573020.13825891X-RAY DIFFRACTION100
1.25-1.270.14963300.13085978X-RAY DIFFRACTION100
1.27-1.290.14162830.1235970X-RAY DIFFRACTION100
1.29-1.310.12622820.12255960X-RAY DIFFRACTION100
1.31-1.340.1383310.11755991X-RAY DIFFRACTION100
1.34-1.360.15063300.11155893X-RAY DIFFRACTION100
1.36-1.390.12943610.115888X-RAY DIFFRACTION99.97
1.39-1.410.11352840.09876027X-RAY DIFFRACTION100
1.41-1.440.10233350.09315916X-RAY DIFFRACTION100
1.45-1.480.1152850.08445982X-RAY DIFFRACTION100
1.48-1.520.1063270.07735944X-RAY DIFFRACTION100
1.52-1.560.10692920.0755994X-RAY DIFFRACTION100
1.56-1.60.0983350.0765896X-RAY DIFFRACTION100
1.6-1.650.10053080.07485939X-RAY DIFFRACTION100
1.65-1.710.09363050.07465992X-RAY DIFFRACTION100
1.71-1.780.10622990.07855960X-RAY DIFFRACTION100
1.78-1.860.10573210.08415935X-RAY DIFFRACTION100
1.86-1.960.10533080.08845950X-RAY DIFFRACTION100
1.96-2.080.10783250.08855964X-RAY DIFFRACTION100
2.08-2.240.10183650.09035910X-RAY DIFFRACTION100
2.24-2.470.10413380.09515936X-RAY DIFFRACTION100
2.47-2.820.12323130.10765904X-RAY DIFFRACTION100
2.83-3.550.12783000.11555983X-RAY DIFFRACTION100
3.56-17.920.13113260.13325823X-RAY DIFFRACTION98.13

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