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- PDB-5jgr: Spin-Labeled T4 Lysozyme Construct K43V1 -

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Basic information

Entry
Database: PDB / ID: 5jgr
TitleSpin-Labeled T4 Lysozyme Construct K43V1
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
HEXANE-1,6-DIOL / : / PHOSPHATE ION / Chem-V1A / Endolysin
Similarity search - Component
Biological speciesEnterobacteria phage T4 sensu lato (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 Å
AuthorsBalo, A.R. / Feyrer, H. / Ernst, O.P.
Funding support Canada, 2items
OrganizationGrant numberCountry
Canada Excellence Research Chairs 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 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2128
Polymers18,6021
Non-polymers6107
Water5,332296
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area950 Å2
ΔGint-23 kcal/mol
Surface area8790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.760, 59.760, 96.259
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: 18602.326 Da / Num. of mol.: 1 / Mutation: K43C, C54T, C97A
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 , 6 types, 303 molecules

#2: 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
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#6: Chemical ChemComp-HEZ / HEXANE-1,6-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C6H14O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 296 / 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: 2.65 Å3/Da / Density % sol: 53.66 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7.2
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: 1.46→51.75 Å / Num. obs: 34628 / % possible obs: 98 % / Redundancy: 2 % / Net I/σ(I): 6.3
Reflection shellHighest resolution: 1.46 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: 1.46→51.75 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 16.7
RfactorNum. reflection% reflection
Rfree0.1928 2007 5.82 %
Rwork0.1664 --
obs0.1679 34463 97.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.46→51.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1306 0 28 296 1630
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011401
X-RAY DIFFRACTIONf_angle_d0.7691894
X-RAY DIFFRACTIONf_dihedral_angle_d19.782554
X-RAY DIFFRACTIONf_chiral_restr0.064210
X-RAY DIFFRACTIONf_plane_restr0.004240
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4578-1.49420.2471950.23211502X-RAY DIFFRACTION64
1.4942-1.53460.19091430.17092338X-RAY DIFFRACTION100
1.5346-1.57980.17551440.15792329X-RAY DIFFRACTION100
1.5798-1.63080.21271450.15682346X-RAY DIFFRACTION100
1.6308-1.68910.16931440.16132342X-RAY DIFFRACTION100
1.6891-1.75670.17991430.15932362X-RAY DIFFRACTION100
1.7567-1.83670.19691470.16522361X-RAY DIFFRACTION100
1.8367-1.93350.18961470.16712380X-RAY DIFFRACTION100
1.9335-2.05470.20551490.16822358X-RAY DIFFRACTION100
2.0547-2.21330.16891450.16392369X-RAY DIFFRACTION100
2.2133-2.4360.19891420.16252400X-RAY DIFFRACTION100
2.436-2.78850.17831510.17472385X-RAY DIFFRACTION100
2.7885-3.51310.20181490.16012443X-RAY DIFFRACTION100
3.5131-51.78620.20011630.16862541X-RAY DIFFRACTION100

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