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- PDB-7xe9: T4 lysozyme mutant-S44C/C54T/N68C/A93C/C97A/T115C, DMSO 20% -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 7xe9
TitleT4 lysozyme mutant-S44C/C54T/N68C/A93C/C97A/T115C, DMSO 20%
ComponentsEndolysin
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 / Phage lysozyme / Lysozyme domain superfamily / Lysozyme-like domain superfamily
Similarity search - Domain/homology
HEXANE-1,6-DIOL / Endolysin
Similarity search - Component
Biological speciesEscherichia virus T4
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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
Revision 1.2Oct 30, 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: Endolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,38110
Polymers18,6681
Non-polymers7139
Water2,666148
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2110 Å2
ΔGint4 kcal/mol
Surface area8260 Å2
Unit cell
Length a, b, c (Å)59.873, 59.873, 96.030
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

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Protein , 1 types, 1 molecules A

#1: Protein Endolysin / 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

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Non-polymers , 6 types, 157 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-HEZ / HEXANE-1,6-DIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 2.66 Å3/Da / Density % sol: 53.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: A crystal was soaked into the precipitant-free solutions containing 20% DMSO.

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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: 1.5→25.93 Å / Num. obs: 32395 / % possible obs: 99.5 % / Redundancy: 10.3 % / Biso Wilson estimate: 21.39 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.054 / Net I/σ(I): 30.7
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 7.7 % / Mean I/σ(I) obs: 3.8 / Num. unique obs: 3067 / CC1/2: 0.949 / Rrim(I) all: 0.465 / % possible all: 95.8

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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: 1.5→25.93 Å / SU ML: 0.1463 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.275
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2324 2003 6.2 %
Rwork0.2016 30287 -
obs0.2035 32290 99.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.4 Å2
Refinement stepCycle: LAST / Resolution: 1.5→25.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1290 0 42 148 1480
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00751424
X-RAY DIFFRACTIONf_angle_d1.21571915
X-RAY DIFFRACTIONf_chiral_restr0.0827208
X-RAY DIFFRACTIONf_plane_restr0.0074242
X-RAY DIFFRACTIONf_dihedral_angle_d10.2102217
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.540.30591360.25182029X-RAY DIFFRACTION93.8
1.54-1.580.27151390.24072099X-RAY DIFFRACTION99.2
1.58-1.630.23551410.23782140X-RAY DIFFRACTION99.17
1.63-1.680.22021370.21722121X-RAY DIFFRACTION99.3
1.68-1.740.22361430.22732152X-RAY DIFFRACTION99.48
1.74-1.810.24721400.22082170X-RAY DIFFRACTION99.78
1.81-1.890.26031460.22752164X-RAY DIFFRACTION99.74
1.89-1.990.23841440.21362161X-RAY DIFFRACTION99.74
1.99-2.110.21191470.2062140X-RAY DIFFRACTION99.83
2.11-2.280.25561460.19512162X-RAY DIFFRACTION100
2.28-2.510.24921470.21242204X-RAY DIFFRACTION99.87
2.51-2.870.20721470.20782195X-RAY DIFFRACTION99.91
2.87-3.610.21231440.18932229X-RAY DIFFRACTION99.71
3.61-25.930.23861460.1872321X-RAY DIFFRACTION98.84

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