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- PDB-7xe5: T4 lysozyme mutant-S44C/C54T/N68C/A93C/C97A/T115C, pH4 -

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Open data


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Basic information

Entry
Database: PDB / ID: 7xe5
TitleT4 lysozyme mutant-S44C/C54T/N68C/A93C/C97A/T115C, pH4
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 / PHOSPHATE ION / Endolysin
Similarity search - Component
Biological speciesEscherichia virus T4
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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)19,2988
Polymers18,6681
Non-polymers6317
Water4,414245
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint-6 kcal/mol
Surface area8800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.295, 60.295, 96.872
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
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 , 5 types, 252 molecules

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


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-HEZ / HEXANE-1,6-DIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / 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: 2.72 Å3/Da / Density % sol: 54.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: A crystal was soaked into precipitant-free solution (pH4)

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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: 1.3→32.3 Å / Num. obs: 50560 / % possible obs: 99.6 % / Redundancy: 10.1 % / Biso Wilson estimate: 13.16 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.081 / Net I/σ(I): 26
Reflection shellResolution: 1.3→1.35 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 2.6 / Num. unique obs: 4785 / CC1/2: 0.84 / Rrim(I) all: 0.591 / % possible all: 95.9

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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: 1.3→32.29 Å / SU ML: 0.1175 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.8723
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1712 1989 3.94 %
Rwork0.1529 48498 -
obs0.1536 50487 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.7 Å2
Refinement stepCycle: LAST / Resolution: 1.3→32.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1307 0 40 245 1592
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061433
X-RAY DIFFRACTIONf_angle_d0.97741933
X-RAY DIFFRACTIONf_chiral_restr0.0695212
X-RAY DIFFRACTIONf_plane_restr0.0066245
X-RAY DIFFRACTIONf_dihedral_angle_d8.533222
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.330.25811310.23083235X-RAY DIFFRACTION94.05
1.33-1.370.23251400.18933418X-RAY DIFFRACTION99.66
1.37-1.410.19411410.15773440X-RAY DIFFRACTION99.8
1.41-1.450.16431380.14263408X-RAY DIFFRACTION99.72
1.45-1.510.1761420.13443466X-RAY DIFFRACTION99.64
1.51-1.570.15731430.12333423X-RAY DIFFRACTION99.8
1.57-1.640.14111400.13183458X-RAY DIFFRACTION99.86
1.64-1.720.15041420.11993462X-RAY DIFFRACTION99.83
1.72-1.830.16751450.14273484X-RAY DIFFRACTION99.86
1.83-1.970.15711380.13723457X-RAY DIFFRACTION100
1.97-2.170.15691460.15153487X-RAY DIFFRACTION99.97
2.17-2.490.17261470.15123518X-RAY DIFFRACTION100
2.49-3.130.16411460.16783541X-RAY DIFFRACTION99.95
3.13-32.290.18251500.1593701X-RAY DIFFRACTION99.66

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