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- PDB-6xc1: Crystal structure of bacteriophage T4 spackle and lysozyme in ort... -

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Basic information

Entry
Database: PDB / ID: 6xc1
TitleCrystal structure of bacteriophage T4 spackle and lysozyme in orthorhombic form
Components
  • Lysozyme
  • Protein spackle
KeywordsHYDROLASE / Lysozyme / spackle
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
ISOPROPYL ALCOHOL / Pre-baseplate central spike protein Gp5 / Protein spackle
Similarity search - Component
Biological speciesEscherichia virus T4
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsShi, K. / Oakland, J.T. / Kurniawan, F. / Moeller, N.H. / Aihara, H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118047 United States
CitationJournal: Commun Biol / Year: 2020
Title: Structural basis of superinfection exclusion by bacteriophage T4 Spackle.
Authors: Shi, K. / Oakland, J.T. / Kurniawan, F. / Moeller, N.H. / Banerjee, S. / Aihara, H.
History
DepositionJun 7, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 16, 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: Lysozyme
C: Protein spackle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5117
Polymers32,2072
Non-polymers3045
Water2,144119
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2880 Å2
ΔGint13 kcal/mol
Surface area11450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.084, 46.172, 129.498
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

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


Mass: 20131.152 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia virus T4 / Production host: Escherichia coli (E. coli) / References: UniProt: P16009, lysozyme
#2: Protein Protein spackle


Mass: 12075.799 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia virus T4 / Gene: sp, 61.3 / Production host: Escherichia coli (E. coli) / References: UniProt: P39230
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H2O
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: 1.91 Å3/Da / Density % sol: 35.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 35% (w/v) polyethylene glycol 3350, 20% 2-propanol, 0.1 M HEPES-NaOH pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.92→46.17 Å / Num. obs: 19371 / % possible obs: 99.3 % / Redundancy: 4.9 % / Biso Wilson estimate: 38.85 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.085 / Net I/σ(I): 10.9
Reflection shellResolution: 1.92→1.97 Å / Rmerge(I) obs: 1.8 / Num. unique obs: 1295 / CC1/2: 0.357

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6x6o, 1wth

6x6o

1wth


Resolution: 1.92→43.49 Å / SU ML: 0.2427 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.9342
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2148 915 4.74 %
Rwork0.1861 18400 -
obs0.1875 19315 98.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.62 Å2
Refinement stepCycle: LAST / Resolution: 1.92→43.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1923 0 20 119 2062
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00342007
X-RAY DIFFRACTIONf_angle_d0.56142698
X-RAY DIFFRACTIONf_chiral_restr0.0382292
X-RAY DIFFRACTIONf_plane_restr0.0042349
X-RAY DIFFRACTIONf_dihedral_angle_d20.8004767
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.92-2.020.34471410.30462562X-RAY DIFFRACTION99.01
2.02-2.150.34281430.26242593X-RAY DIFFRACTION99.78
2.15-2.310.24581300.2292617X-RAY DIFFRACTION99.57
2.31-2.550.24771170.20692629X-RAY DIFFRACTION99.53
2.55-2.910.24241200.19662639X-RAY DIFFRACTION99.28
2.92-3.670.22331260.17692636X-RAY DIFFRACTION98.36
3.67-43.490.16771380.1572724X-RAY DIFFRACTION96.4
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.361124431414.13486580875-0.5954798455398.36148063670.1107747198330.868745183216-0.198006374455-0.08374194860530.0651468175527-0.761071621549-0.125719760915-0.0646226999669-0.1219607685260.1468040357540.335081351640.436038672580.0348335038478-0.02196042003130.348810811402-0.002515765409780.23721638558517.565121944714.41079754417.4307174921
20.971935160451.158451765860.9368479628653.222429334383.814420295962.16975015276-0.3519700227730.2567099629280.197583113961-1.031643000170.0622218816310.231869297326-1.009254600160.1723250712160.1850699751550.568964875814-0.0482123047041-0.1054909360670.360748467890.02407720309090.2993116646498.752267954370.03260489426263.03334920953
38.878089739197.813748507813.418590318177.486274455672.140333370758.671560609770.0579692683314-0.4205411110460.8832656757710.319150289571-0.2885801569631.04658524448-0.490345096853-0.7839614584370.1999416856640.4120275499140.05608833053920.05205510501960.417720220264-0.09940805432470.4791816712677.322816498539.8758843437430.4348246793
46.258580318575.95831873738-4.298286921039.23223559433-5.470319469446.40818423460.379454647003-0.327265809465-0.2161848673210.723490158649-0.5170562619-0.311387190652-0.201134899689-0.3123423847150.1303597834150.3499862566340.00188035570317-0.02941014373320.450444663889-0.0301728406610.26693043423112.7406762416-3.6339700801230.7329116469
56.07701092045.9670607454-6.102430957696.1170759277-6.117584501646.361015129280.0161436793967-0.0577376641018-0.2674758673180.4398433831810.201554046561-0.2443763587630.0563224041718-0.0792203806206-0.1395523348190.3568343966640.00326875458068-0.04572875130350.4333518999010.005061536681610.37763687141715.469014868-11.342108622722.9997070954
69.82740036763-0.489420698472-6.642942578467.490131983043.176255142027.016380272570.2151187746810.0324579530378-0.0979120851224-0.0833847009204-0.3126347807380.473483083189-0.423563538301-0.4697117824990.1121290324950.3820220993750.0438890595763-0.06511062198270.394725506578-0.0122827112250.2785932198035.311216632982.7387496323223.8548661893
75.09767635655-4.5665795707-3.81412824678.915005840581.224247101183.9971825816-0.1132159250960.614781025607-0.563594836579-0.291039306967-0.2805466289870.5755611622040.915895339208-0.9161192662010.4457719496190.374974175513-0.0861306926649-0.0542067479520.414094204864-0.04902370577390.3124837955895.63264736764-8.4694067969621.013968375
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 175 through 237 )AA175 - 2371 - 64
22chain 'A' and (resid 238 through 341 )AA238 - 34165 - 169
33chain 'C' and (resid 23 through 36 )CE23 - 361 - 15
44chain 'C' and (resid 37 through 55 )CE37 - 5516 - 35
55chain 'C' and (resid 56 through 70 )CE56 - 7036 - 50
66chain 'C' and (resid 71 through 86 )CE71 - 8651 - 67
77chain 'C' and (resid 87 through 98 )CE87 - 9868 - 79

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