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- PDB-5jgn: Spin-Labeled T4 Lysozyme Construct I9V1 -

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Basic information

Entry
Database: PDB / ID: 5jgn
TitleSpin-Labeled T4 Lysozyme Construct I9V1
ComponentsEndolysinLysin
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 / Lysozyme domain superfamily / Phage lysozyme / 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 / MOLECULAR REPLACEMENT / Resolution: 1.534 Å
AuthorsBalo, A.R. / Feyrer, H. / Ernst, O.P.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canada Excellence Research Chairs 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 1.1Oct 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 1.2Sep 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

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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)19,1468
Polymers18,6181
Non-polymers5277
Water5,981332
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area830 Å2
ΔGint-31 kcal/mol
Surface area8760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.820, 59.820, 95.672
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 / Lysin / Lysis protein / Lysozyme / Muramidase


Mass: 18618.348 Da / Num. of mol.: 1 / Mutation: I9C, 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 , 5 types, 339 molecules

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


Mass: 35.453 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Cl
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: 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
#5: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 332 / 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: 2.65 Å3/Da / Density % sol: 53.66 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop
Details: sodium/potassium phosphate, sodium chloride, hexane-1,6-diol, 2-propanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU / Detector: CCD / Date: Sep 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.534→29.91 Å / Num. obs: 30273 / % possible obs: 100 % / Redundancy: 2 % / Net I/σ(I): 20.09
Reflection shellHighest resolution: 1.534 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: 1.534→29.91 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.38
RfactorNum. reflection% reflection
Rfree0.1717 1991 6.58 %
Rwork0.1517 --
obs0.153 30272 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.534→29.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1307 0 21 332 1660
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061382
X-RAY DIFFRACTIONf_angle_d0.8011873
X-RAY DIFFRACTIONf_dihedral_angle_d9.175863
X-RAY DIFFRACTIONf_chiral_restr0.046206
X-RAY DIFFRACTIONf_plane_restr0.005238
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5341-1.57240.27841370.21221970X-RAY DIFFRACTION100
1.5724-1.61490.18651400.16212001X-RAY DIFFRACTION100
1.6149-1.66250.2071360.15221984X-RAY DIFFRACTION100
1.6625-1.71610.1721420.14281987X-RAY DIFFRACTION100
1.7161-1.77740.18091420.14441985X-RAY DIFFRACTION100
1.7774-1.84860.19421450.1542003X-RAY DIFFRACTION100
1.8486-1.93270.20791440.16371992X-RAY DIFFRACTION100
1.9327-2.03460.19641390.15512017X-RAY DIFFRACTION100
2.0346-2.1620.18841440.14732004X-RAY DIFFRACTION100
2.162-2.32890.16231400.1482013X-RAY DIFFRACTION100
2.3289-2.56320.16311440.15412037X-RAY DIFFRACTION100
2.5632-2.93380.16781410.15252050X-RAY DIFFRACTION100
2.9338-3.69520.14831440.13732067X-RAY DIFFRACTION100
3.6952-29.91570.14531530.15332171X-RAY DIFFRACTION100

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