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- PDB-5ki3: PSEUDO T4 LYSOZYME MUTANT - Y18PHE-BR -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 5ki3
TitlePSEUDO T4 LYSOZYME MUTANT - Y18PHE-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: 1.65 Å
AuthorsButta, H.W. / Scholfield, 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 1.3Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 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 1.6Nov 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
Water4,324240
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.589, 59.589, 95.150
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-307-

HOH

21A-436-

HOH

31A-530-

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.: 240 / 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: 2.64 Å3/Da / Density % sol: 53.43 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 2.0M KPO4, 50MM 2-HYDROXYETHYLDISULFIDE, 50MM 2-MERCAPTOETHANOL, PH 6.7
PH range: 6.7

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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: Jul 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→45.4 Å / Num. obs: 23668 / % possible obs: 98 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.21 / Net I/σ(I): 4.6
Reflection shellResolution: 1.65→1.71 Å / Rmerge(I) obs: 0.759 / Mean I/σ(I) obs: 1 / Num. measured obs: 2084 / % possible all: 92

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Processing

Software
NameVersionClassification
d*TREK9.9.9.6Ldata scaling
d*TREK9.9.9.6Ldata reduction
PHASERphasing
PHENIXDEV_1839refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1L63

1l63


Resolution: 1.65→45.4 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.46 / Phase error: 25.32
RfactorNum. reflection% reflection
Rfree0.25 2010 8.49 %
Rwork0.2 --
obs0.21 23667 98.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 19.72 Å2
Refinement stepCycle: LAST / Resolution: 1.65→45.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1292 0 8 240 1540
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071406
X-RAY DIFFRACTIONf_angle_d0.9671904
X-RAY DIFFRACTIONf_dihedral_angle_d12.164567
X-RAY DIFFRACTIONf_chiral_restr0.041210
X-RAY DIFFRACTIONf_plane_restr0.004243
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.69130.351250.371362X-RAY DIFFRACTION87
1.6913-1.7370.411260.331412X-RAY DIFFRACTION92
1.737-1.78810.351440.311513X-RAY DIFFRACTION97
1.7881-1.84580.331390.281547X-RAY DIFFRACTION99
1.8458-1.91180.311440.261540X-RAY DIFFRACTION99
1.9118-1.98830.31460.231555X-RAY DIFFRACTION99
1.9883-2.07880.251420.191560X-RAY DIFFRACTION99
2.0788-2.18840.241450.181553X-RAY DIFFRACTION100
2.1884-2.32550.231450.181557X-RAY DIFFRACTION100
2.3255-2.50510.251450.191572X-RAY DIFFRACTION100
2.5051-2.75720.241500.21581X-RAY DIFFRACTION100
2.7572-3.1560.251500.191585X-RAY DIFFRACTION100
3.156-3.97590.21530.161629X-RAY DIFFRACTION100
3.9759-45.40.211560.191691X-RAY DIFFRACTION100

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