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- PDB-6pgz: MTSL labelled T4 lysozyme pseudo-wild type V75C mutant -

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Basic information

Entry
Database: PDB / ID: 6pgz
TitleMTSL labelled T4 lysozyme pseudo-wild type V75C mutant
ComponentsEndolysinLysin
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 / Lysozyme domain superfamily / Phage lysozyme / Lysozyme-like domain superfamily
Similarity search - Domain/homology
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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endolysin
B: Endolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8295
Polymers37,2652
Non-polymers5643
Water1,22568
1
A: Endolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9323
Polymers18,6321
Non-polymers3002
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Endolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8972
Polymers18,6321
Non-polymers2641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.941, 53.328, 58.607
Angle α, β, γ (deg.)90.000, 102.930, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and resid 1 through 162)
21(chain B and resid 1 through 162)

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LYS / End label comp-ID: LYS / Auth seq-ID: 1 - 162 / Label seq-ID: 1 - 162

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1(chain A and resid 1 through 162)AA
2(chain B and resid 1 through 162)BB

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Components

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


Mass: 18632.375 Da / Num. of mol.: 2 / Mutation: C54T, V75C, 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-MTN / S-[(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl] methanesulfonothioate / MTSL / MTSL


Mass: 264.385 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H18NO3S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 2.14 Å3/Da / Density % sol: 42.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 2.0M Na/K Phosphate, 250mM NaCl, pH7.0

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Data collection

DiffractionMean temperature: 100 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→50 Å / Num. obs: 19008 / % possible obs: 89.1 % / Redundancy: 2.8 % / Biso Wilson estimate: 22.6 Å2 / Rmerge(I) obs: 0.074 / Χ2: 0.85 / Net I/av σ(I): 11.7 / Net I/σ(I): 12.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsΧ2% possible all
2-2.072.80.2773.321400.706100
2.07-2.152.80.2221020.811100
2.15-2.252.70.20514190.88966.7
2.25-2.372.70.15216450.90478.3
2.37-2.522.80.12621140.93899.9
2.52-2.712.80.10121300.87899.6
2.71-2.992.90.08521150.91899.2
2.99-3.422.90.0721030.90598.8
3.42-4.312.80.06411470.87453.2
4.31-502.90.04820930.71395.1

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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→14.955 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 32.66
RfactorNum. reflection% reflection
Rfree0.2913 890 5 %
Rwork0.2531 --
obs0.255 17794 83.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 63.74 Å2 / Biso mean: 24.7278 Å2 / Biso min: 5.89 Å2
Refinement stepCycle: final / Resolution: 2→14.955 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2598 0 25 68 2691
Biso mean--23.81 23.55 -
Num. residues----326
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A992X-RAY DIFFRACTION0.769TORSIONAL
12B992X-RAY DIFFRACTION0.769TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.1250.34981320.28452518265075
2.125-2.28860.38321060.29392007211360
2.2886-2.51790.33041750.2813317349299
2.5179-2.880.29871750.27723338351399
2.88-3.61990.27681700.25143210338098
3.6199-14.95520.24291320.20812514264683

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