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- PDB-5ki8: PSEUDO T4 LYSOZYME MUTANT - Y88PHE-BR -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 5ki8
TitlePSEUDO T4 LYSOZYME MUTANT - Y88PHE-BR
ComponentsEndolysin
KeywordsHYDROLASE / HALOGEN BONDS / T4 LYSOZYME
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
2-HYDROXYETHYL DISULFIDE / Endolysin
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsScholfield, M.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-1152494 United States
CitationJournal: Biochemistry / Year: 2017
Title: Structure-Energy Relationships of Halogen Bonds in Proteins.
Authors: Scholfield, M.R. / Ford, M.C. / Carlsson, A.C. / Butta, H. / Mehl, R.A. / Ho, P.S.
History
DepositionJun 16, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2017Group: Database references
Revision 1.2Jun 14, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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)19,6742
Polymers19,5201
Non-polymers1541
Water3,549197
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.013, 60.013, 95.945
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-412-

HOH

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Components

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


Mass: 19520.141 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Plasmid: PBAD / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BH10B / References: UniProt: P00720, lysozyme
#2: Chemical ChemComp-HED / 2-HYDROXYETHYL DISULFIDE


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / Source method: isolated from a natural source / Formula: H2O

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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: 54.47 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: 2.4M KPO4, 50MM 2-HYDROXYETHYLDISULFIDE, 50MM 2-MERCAPTOETHANOL, PH 6.9
PH range: 6.9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Apr 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→45.7 Å / Num. obs: 28167 / % possible obs: 95 % / Redundancy: 1.9 % / Biso Wilson estimate: 20.64 Å2 / Rmerge(I) obs: 0.026 / Net I/σ(I): 16.1
Reflection shellResolution: 1.55→1.61 Å / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 6.3 / Num. measured obs: 2068 / % possible all: 71

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Processing

Software
NameVersionClassification
d*TREK9.9.9.4Ldata scaling
PHASERphasing
PHENIXDEV_1951refinement
d*TREK9.9.9.4Ldata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1L63

1l63


Resolution: 1.55→45.7 Å / SU ML: 0.169 / Cross valid method: FREE R-VALUE / σ(F): 1.43 / Phase error: 22.22
RfactorNum. reflection% reflection
Rfree0.21 1993 7.088 %
Rwork0.176 --
obs0.178 28118 94.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 24.62 Å2
Refinement stepCycle: LAST / Resolution: 1.55→45.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1292 0 8 197 1497
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061405
X-RAY DIFFRACTIONf_angle_d0.9911904
X-RAY DIFFRACTIONf_dihedral_angle_d12.4563
X-RAY DIFFRACTIONf_chiral_restr0.044209
X-RAY DIFFRACTIONf_plane_restr0.004247
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.58880.341030.281310X-RAY DIFFRACTION67
1.5888-1.63180.311180.281566X-RAY DIFFRACTION81
1.6318-1.67980.261390.241849X-RAY DIFFRACTION96
1.6798-1.7340.231440.211875X-RAY DIFFRACTION97
1.734-1.7960.311470.21891X-RAY DIFFRACTION97
1.796-1.86790.231420.191898X-RAY DIFFRACTION97
1.8679-1.95290.241460.191909X-RAY DIFFRACTION98
1.9529-2.05590.231460.181911X-RAY DIFFRACTION98
2.0559-2.18470.191520.161917X-RAY DIFFRACTION98
2.1847-2.35330.191410.161954X-RAY DIFFRACTION99
2.3533-2.59020.211500.171949X-RAY DIFFRACTION99
2.5902-2.96490.21520.171984X-RAY DIFFRACTION99
2.9649-3.73520.21540.162005X-RAY DIFFRACTION100
3.7352-45.70.191590.172107X-RAY DIFFRACTION99

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