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- PDB-5jgu: Spin-Labeled T4 Lysozyme Construct R119V1 -

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Basic information

Entry
Database: PDB / ID: 5jgu
TitleSpin-Labeled T4 Lysozyme Construct R119V1
ComponentsEndolysin
KeywordsHYDROLASE / Spin label / EPR / DEER
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
: / PHOSPHATE ION / Chem-V1A / Endolysin
Similarity search - Component
Biological speciesEnterobacteria phage T4 sensu lato (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.468 Å
AuthorsBalo, A.R. / Feyrer, H. / Ernst, O.P.
Funding support Canada, 2items
OrganizationGrant numberCountry
Canada Excellence Research Chair Program Canada
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: Biochemistry / Year: 2016
Title: Toward Precise Interpretation of DEER-Based Distance Distributions: Insights from Structural Characterization of V1 Spin-Labeled Side Chains.
Authors: Balo, A.R. / Feyrer, H. / Ernst, O.P.
History
DepositionApr 20, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 25, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
Revision 1.5May 1, 2024Group: Advisory / Derived calculations
Category: pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_conn_type
Item: _struct_conn.conn_type_id / _struct_conn.id ..._struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn_type.id
Revision 1.6Oct 16, 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)19,0667
Polymers18,5741
Non-polymers4926
Water5,513306
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area770 Å2
ΔGint-30 kcal/mol
Surface area8810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.919, 59.919, 96.154
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 18574.311 Da / Num. of mol.: 1 / Mutation: C54T, C97A, R119C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 sensu lato (virus)
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P00720, lysozyme

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Non-polymers , 5 types, 312 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-V1A / S-(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-imidazol-4-yl) methanesulfonothioate


Mass: 251.346 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15N2O3S2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 306 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.68 Å3/Da / Density % sol: 54.15 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: sodium/potassium phosphate, sodium chloride, hexane-1,6-diol, 2-propanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 19, 2015
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.468→45.67 Å / Num. obs: 33872 / % possible obs: 97 % / Redundancy: 2 % / Net I/σ(I): 25.02
Reflection shellHighest resolution: 1.468 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1C6T

1c6t


Resolution: 1.468→45.666 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 15.06
RfactorNum. reflection% reflection
Rfree0.1746 2009 5.93 %
Rwork0.1513 --
obs0.1527 33870 97.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.468→45.666 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1304 0 20 306 1630
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081378
X-RAY DIFFRACTIONf_angle_d0.7811862
X-RAY DIFFRACTIONf_dihedral_angle_d13.627535
X-RAY DIFFRACTIONf_chiral_restr0.064208
X-RAY DIFFRACTIONf_plane_restr0.005235
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4685-1.50520.1561380.14812151X-RAY DIFFRACTION93
1.5052-1.54590.18591350.14642222X-RAY DIFFRACTION96
1.5459-1.59140.16251410.14032201X-RAY DIFFRACTION96
1.5914-1.64280.17221390.14662219X-RAY DIFFRACTION97
1.6428-1.70150.17311400.14422246X-RAY DIFFRACTION97
1.7015-1.76960.16121430.14532247X-RAY DIFFRACTION97
1.7696-1.85020.18451430.15252227X-RAY DIFFRACTION97
1.8502-1.94770.17451450.15442265X-RAY DIFFRACTION98
1.9477-2.06970.16951380.15042286X-RAY DIFFRACTION98
2.0697-2.22950.18051440.14612293X-RAY DIFFRACTION98
2.2295-2.45390.1831510.15392300X-RAY DIFFRACTION99
2.4539-2.80890.17921440.16412340X-RAY DIFFRACTION99
2.8089-3.53880.17131450.14692383X-RAY DIFFRACTION99
3.5388-45.68790.17451630.15472481X-RAY DIFFRACTION100

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