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- PDB-6pgy: MTSL labelled T4 lysozyme pseudo-wild type K65C mutant -

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Basic information

Entry
Database: PDB / ID: 6pgy
TitleMTSL labelled T4 lysozyme pseudo-wild type K65C mutant
ComponentsEndolysin
KeywordsHYDROLASE / T4 Lysozyme / MTSL / spin label
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 / Chem-MTN / Endolysin
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsCuneo, M.J. / Myles, D.A. / Li, L.
CitationJournal: To be published
Title: Making hydrogens stand out: Enhanced neutron diffraction from biological crystals using dynamic nuclear polarization
Authors: Pierce, J. / Myles, D.A.
History
DepositionJun 25, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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)19,0925
Polymers18,6021
Non-polymers4904
Water1,63991
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: Many years of literature shows this.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.020, 61.020, 96.481
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 18602.326 Da / Num. of mol.: 1 / Mutation: C54T, K65C, C97A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Gene: e, T4Tp126 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: D9IEF7, lysozyme
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-MTN / S-[(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl] methanesulfonothioate / MTSL


Mass: 264.385 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H18NO3S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-HED / 2-HYDROXYETHYL DISULFIDE


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.79 Å3/Da / Density % sol: 55.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8 / Details: 2.0M Na/K phosphate

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 14595 / % possible obs: 100 % / Redundancy: 6.9 % / Biso Wilson estimate: 29.43 Å2 / Rmerge(I) obs: 0.111 / Χ2: 1.322 / Net I/av σ(I): 17.8 / Net I/σ(I): 10.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsΧ2% possible all
2-2.076.10.5553.514331.134100
2.07-2.156.90.4114241.322100
2.15-2.2570.32314261.382100
2.25-2.3770.25714231.494100
2.37-2.527.10.22714591.536100
2.52-2.717.10.19114471.589100
2.71-2.997.10.14614551.43599.9
2.99-3.427.10.11614621.219100
3.42-4.3170.08614881.222100
4.31-406.70.05915780.864100

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VNR

5vnr


Resolution: 2→35.628 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.18
RfactorNum. reflection% reflectionSelection details
Rfree0.1817 729 5.01 %Random
Rwork0.1582 ---
obs0.1594 14564 99.99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 88.01 Å2 / Biso mean: 30.6463 Å2 / Biso min: 16.8 Å2
Refinement stepCycle: final / Resolution: 2→35.628 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1289 0 22 91 1402
Biso mean--58.77 39.64 -
Num. residues----162
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2-2.15430.2531440.20327192863
2.1543-2.37110.21241400.171926992839
2.3711-2.71410.23371440.172927582902
2.7141-3.4190.19731480.168327652913
3.419-35.63360.13771530.136828943047

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