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- PDB-7xe6: T4 lysozyme mutant-S44C/C54T/N68C/A93C/C97A/T115C, pH7 -

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Basic information

Entry
Database: PDB / ID: 7xe6
TitleT4 lysozyme mutant-S44C/C54T/N68C/A93C/C97A/T115C, pH7
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
Lysozyme - #40 / Endolysin T4 type / 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
HEXANE-1,6-DIOL / Endolysin
Similarity search - Component
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
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: Endolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1578
Polymers18,6681
Non-polymers4907
Water5,711317
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-12 kcal/mol
Surface area8690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.999, 59.999, 97.101
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 / 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-HEZ / HEXANE-1,6-DIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 317 / 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: 2.7 Å3/Da / Density % sol: 54.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: A crystal was soaked into precipitant-free solutions (pH7).

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 25, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.1→45.9 Å / Num. obs: 82294 / % possible obs: 99.5 % / Redundancy: 9.6 % / Biso Wilson estimate: 9.97 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.066 / Net I/σ(I): 21
Reflection shellResolution: 1.1→1.14 Å / Mean I/σ(I) obs: 2.5 / Num. unique obs: 8082 / CC1/2: 0.891 / Rrim(I) all: 0.609

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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→25.52 Å / SU ML: 0.0786 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.6835
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1679 1994 2.43 %
Rwork0.1484 80196 -
obs0.1488 82190 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.06 Å2
Refinement stepCycle: LAST / Resolution: 1.1→25.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1307 0 31 317 1655
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00611441
X-RAY DIFFRACTIONf_angle_d1.00121947
X-RAY DIFFRACTIONf_chiral_restr0.0781213
X-RAY DIFFRACTIONf_plane_restr0.009249
X-RAY DIFFRACTIONf_dihedral_angle_d10.2939223
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1-1.130.1831410.18185620X-RAY DIFFRACTION98.53
1.13-1.160.17021410.15355653X-RAY DIFFRACTION99.31
1.16-1.190.17151380.14475662X-RAY DIFFRACTION99.28
1.19-1.230.13751450.14025692X-RAY DIFFRACTION99.66
1.23-1.270.14981410.14475683X-RAY DIFFRACTION99.47
1.27-1.330.16961440.12775678X-RAY DIFFRACTION99.79
1.33-1.390.16211420.13435725X-RAY DIFFRACTION99.81
1.39-1.460.14291400.12975727X-RAY DIFFRACTION99.83
1.46-1.550.17041480.13385757X-RAY DIFFRACTION99.93
1.55-1.670.14071420.12825741X-RAY DIFFRACTION99.98
1.67-1.840.16771460.15195776X-RAY DIFFRACTION99.97
1.84-2.10.16411430.15025788X-RAY DIFFRACTION99.76
2.1-2.650.16351450.15665861X-RAY DIFFRACTION99.9
2.65-25.520.18841380.15615833X-RAY DIFFRACTION95.81

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