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- PDB-5ki2: PSEUDO T4 LYSOZYME MUTANT - Y18PHE-METHYL -

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Basic information

Entry
Database: PDB / ID: 5ki2
TitlePSEUDO T4 LYSOZYME MUTANT - Y18PHE-METHYL
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: 1.5 Å
AuthorsFord, M.C. / 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 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)19,6102
Polymers19,4551
Non-polymers1541
Water6,467359
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.197, 60.197, 95.969
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-460-

HOH

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Components

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


Mass: 19455.271 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.: 359 / Source method: isolated from a natural source / Formula: H2O
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: 2.73 Å3/Da / Density % sol: 54.92 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 2.2M KPO4, 50MM 2-HYDROXYETHYLDISULFIDE, 50MM 2-MERCAPTOETHANOL, PH 6.8
PH range: 6.8

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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: Jan 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.499→18.76 Å / Num. obs: 31673 / % possible obs: 96 % / Redundancy: 9.8 % / Biso Wilson estimate: 13.92 Å2 / Rmerge(I) obs: 0.115 / Net I/σ(I): 23.1
Reflection shellResolution: 1.499→1.55 Å / Rmerge(I) obs: 0.757 / Mean I/σ(I) obs: 1.8 / Num. measured obs: 2670 / % possible all: 67

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Processing

Software
NameVersionClassification
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
PHENIXDEV_1839refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1L63

1l63


Resolution: 1.5→18.76 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.68
RfactorNum. reflection% reflection
Rfree0.221 1864 6.3 %
Rwork0.188 --
obs0.19 27530 96.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 19.1 Å2
Refinement stepCycle: LAST / Resolution: 1.5→18.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1292 0 8 359 1659
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061424
X-RAY DIFFRACTIONf_angle_d1.0141932
X-RAY DIFFRACTIONf_dihedral_angle_d12.496571
X-RAY DIFFRACTIONf_chiral_restr0.035212
X-RAY DIFFRACTIONf_plane_restr0.004251
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.499-1.53650.3361140.2851651X-RAY DIFFRACTION76
1.5365-1.57810.2831410.252136X-RAY DIFFRACTION98
1.5781-1.62450.2421420.2172120X-RAY DIFFRACTION98
1.6245-1.67690.2231480.2112152X-RAY DIFFRACTION99
1.6769-1.73680.2471480.1982124X-RAY DIFFRACTION99
1.7368-1.80630.2481470.2182166X-RAY DIFFRACTION99
1.8063-1.88840.2461460.2412170X-RAY DIFFRACTION99
1.8884-1.98790.3321470.2532162X-RAY DIFFRACTION99
1.9879-2.11230.2081470.1912180X-RAY DIFFRACTION100
2.1123-2.27510.2341450.1872179X-RAY DIFFRACTION99
2.2751-2.50370.2111460.1752206X-RAY DIFFRACTION99
2.5037-2.86490.1931470.1712237X-RAY DIFFRACTION100
2.8649-3.60570.1951460.1522197X-RAY DIFFRACTION98
3.6057-18.760.1861350.1611968X-RAY DIFFRACTION83

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