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- PDB-5kio: PSEUDO T4 LYSOZYME MUTANT - Y18PHE-I -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 5kio
TitlePSEUDO T4 LYSOZYME MUTANT - Y18PHE-I
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 / MOLECULAR REPLACEMENT / Resolution: 1.63 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 1.3Sep 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 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)19,7212
Polymers19,5671
Non-polymers1541
Water4,612256
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.103, 60.103, 96.080
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Components on special symmetry positions
IDModelComponents
11A-453-

HOH

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Components

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


Mass: 19567.143 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.: 256 / 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: ROTATING ANODE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.54 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jul 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.63→32.03 Å / Num. obs: 25701 / % possible obs: 99 % / Redundancy: 8.5 % / Biso Wilson estimate: 16.74 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 31
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.63-1.6660.7921100
1.66-1.696.20.73199.9
1.69-1.726.30.588199.9
1.72-1.766.40.568199.9
1.76-1.796.60.5191100
1.79-1.846.70.441100
1.84-1.886.60.563199.9
1.88-1.936.60.4171100
1.93-1.996.90.37199.9
1.99-2.057.20.2131100
2.05-2.137.30.2131100
2.13-2.216.90.201199.7
2.21-2.3170.26199.8
2.31-2.4380.119199.9
2.43-2.598.70.1031100
2.59-2.799.50.0941100
2.79-3.0710.60.0781100
3.07-3.5112.10.071100
3.51-4.4214.10.0671100
4.42-5018.70.063199.6

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Processing

Software
NameVersionClassification
PHENIXdev_1951refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
d*TREK9.9.9.6Ldata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1L63

1l63


Resolution: 1.63→32.03 Å / SU ML: 0.199 / Cross valid method: FREE R-VALUE / σ(F): 1.335 / Phase error: 23.717
RfactorNum. reflection% reflection
Rfree0.237 1784 7.8 %
Rwork0.191 --
obs0.195 25541 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 19.1 Å2
Refinement stepCycle: LAST / Resolution: 1.63→32.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1292 0 8 256 1556
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00641409
X-RAY DIFFRACTIONf_angle_d1.04841914
X-RAY DIFFRACTIONf_chiral_restr0.0435212
X-RAY DIFFRACTIONf_plane_restr0.0048247
X-RAY DIFFRACTIONf_dihedral_angle_d11.926566
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.63-1.6690.31370.2261631X-RAY DIFFRACTION98.16
1.669-1.71420.291420.2111655X-RAY DIFFRACTION99.94
1.7142-1.76460.271400.2221680X-RAY DIFFRACTION99.94
1.7646-1.82160.31400.2211684X-RAY DIFFRACTION100
1.8216-1.88660.311360.2571612X-RAY DIFFRACTION97.49
1.8866-1.96220.371360.3141646X-RAY DIFFRACTION98.78
1.9622-2.05150.261430.2051680X-RAY DIFFRACTION99.89
2.0515-2.15960.261430.191691X-RAY DIFFRACTION99.83
2.1596-2.29490.31360.2321643X-RAY DIFFRACTION97.32
2.2949-2.4720.241430.1921663X-RAY DIFFRACTION98.31
2.472-2.72060.21470.1831709X-RAY DIFFRACTION99.84
2.7206-3.1140.221420.1771699X-RAY DIFFRACTION99.78
3.114-3.92230.21460.1531735X-RAY DIFFRACTION99.68
3.9223-32.030.181600.1561822X-RAY DIFFRACTION99.7

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