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- PDB-7xea: T4 lysozyme mutant-S44C/C54T/N68C/A93C/C97A/T115C, DMSO 40%, and ... -

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Basic information

Entry
Database: PDB / ID: 7xea
TitleT4 lysozyme mutant-S44C/C54T/N68C/A93C/C97A/T115C, DMSO 40%, and then backsoaking
ComponentsEndolysinLysin
KeywordsHYDROLASE / Intermolecular disulfide symmetry cross-linked crystal
Function / homology
Function and homology information


viral release from host cell by cytolysis / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / host cell cytoplasm / defense response to bacterium
Similarity search - Function
Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / Lysozyme-like domain superfamily
Similarity search - Domain/homology
Biological speciesEscherichia virus T4
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsTamada, T. / Hiromoto, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Front Mol Biosci / Year: 2022
Title: Creation of Cross-Linked Crystals With Intermolecular Disulfide Bonds Connecting Symmetry-Related Molecules Allows Retention of Tertiary Structure in Different Solvent Conditions.
Authors: Hiromoto, T. / Ikura, T. / Honjo, E. / Blaber, M. / Kuroki, R. / Tamada, T.
History
DepositionMar 30, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 22, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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: Endolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0159
Polymers18,6681
Non-polymers3478
Water4,864270
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-11 kcal/mol
Surface area8760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.898, 59.898, 96.770
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#1: Protein Endolysin / Lysin / Lysis protein / Lysozyme / Muramidase


Mass: 18667.572 Da / Num. of mol.: 1 / Mutation: S44C, C54T, N68C, A93C, C97A, T115C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia virus T4 / Gene: e, T4Tp126 / Production host: Escherichia coli (E. coli) / References: UniProt: D9IEF7, lysozyme
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 270 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.68 Å3/Da / Density % sol: 54.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: A crystal was soaked into the precipitant-free solutions containing 40% DMSO, and then backsoaked into the precipitant-free solution.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 6, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.1→35.4 Å / Num. obs: 81025 / % possible obs: 98.7 % / Redundancy: 9.8 % / Biso Wilson estimate: 11.94 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.062 / Net I/σ(I): 23.3
Reflection shellResolution: 1.1→1.14 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 7157 / CC1/2: 0.812 / Rrim(I) all: 0.63 / % possible all: 88.4

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VNR

5vnr


Resolution: 1.1→25.05 Å / SU ML: 0.0875 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.7436
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1813 1990 2.46 %
Rwork0.159 78742 -
obs0.1595 80732 98.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.84 Å2
Refinement stepCycle: LAST / Resolution: 1.1→25.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1298 0 18 270 1586
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00611466
X-RAY DIFFRACTIONf_angle_d0.93791988
X-RAY DIFFRACTIONf_chiral_restr0.0735216
X-RAY DIFFRACTIONf_plane_restr0.0075258
X-RAY DIFFRACTIONf_dihedral_angle_d7.5409225
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1-1.130.23851200.23454788X-RAY DIFFRACTION84.36
1.13-1.160.21171350.19015477X-RAY DIFFRACTION97.55
1.16-1.190.19171430.16375623X-RAY DIFFRACTION99.26
1.19-1.230.17761480.15495607X-RAY DIFFRACTION99.31
1.23-1.270.17881390.15795655X-RAY DIFFRACTION99.69
1.27-1.330.18781450.14325662X-RAY DIFFRACTION99.59
1.33-1.390.16371410.14615642X-RAY DIFFRACTION99.67
1.39-1.460.1521470.145696X-RAY DIFFRACTION99.86
1.46-1.550.15631410.14025647X-RAY DIFFRACTION99.84
1.55-1.670.13191440.13715733X-RAY DIFFRACTION99.83
1.67-1.840.18091440.16485713X-RAY DIFFRACTION99.88
1.84-2.10.18361420.15825748X-RAY DIFFRACTION99.86
2.1-2.650.17211480.16285806X-RAY DIFFRACTION99.8
2.65-25.050.19951530.16295945X-RAY DIFFRACTION98.59

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