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- PDB-2nth: Structure of Spin-labeled T4 Lysozyme Mutant L118R1 -

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Basic information

Entry
Database: PDB / ID: 2nth
TitleStructure of Spin-labeled T4 Lysozyme Mutant L118R1
ComponentsLysozyme
KeywordsHYDROLASE / Nitroxide / Spin label / T4 lysozyme / Electron paramagnetic resonance / EPR
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
Lysozyme - #40 / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / Lysozyme / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-MTN / Endolysin
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsGuo, Z. / Cascio, D. / Hideg, K. / Hubbell, W.L.
CitationJournal: Protein Sci. / Year: 2007
Title: Structural determinants of nitroxide motion in spin-labeled proteins: Tertiary contact and solvent-inaccessible sites in helix G of T4 lysozyme.
Authors: Guo, Z. / Cascio, D. / Hideg, K. / Kalai, T. / Hubbell, W.L.
History
DepositionNov 7, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 27, 2011Group: Non-polymer description
Revision 1.4Oct 18, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.5Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8832
Polymers18,6181
Non-polymers2641
Water3,351186
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.761, 59.761, 95.005
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 18618.348 Da / Num. of mol.: 1 / Mutation: C54T, C97A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Genus: T4-like viruses / Species: Enterobacteria phage T4 sensu lato / Gene: E / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P00720, 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.: 1 / Source method: obtained synthetically / Formula: C10H18NO3S2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 2.6 Å3/Da / Density % sol: 52.77 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 2.0 M Na/K Phosphate, 240 mM NaCl, 40 mM 2-hydroxyethyl disulfide, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 4, 2002 / Details: Parabolic collimating mirrors
RadiationMonochromator: Sagitally Focused Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.8→100 Å / Num. all: 18745 / Num. obs: 18745 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.2 % / Rsym value: 0.081 / Net I/σ(I): 20.4
Reflection shellResolution: 1.8→1.86 Å / Mean I/σ(I) obs: 4.2 / Rsym value: 0.434 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LZM

3lzm


Resolution: 1.8→35 Å / FOM work R set: 0.875 / Cross valid method: Free R / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.212 970 5.2 %Random
Rwork0.183 ---
all0.195 18733 --
obs0.195 18733 99.8 %-
Solvent computationBsol: 46.33 Å2
Displacement parametersBiso mean: 19.087 Å2
Baniso -1Baniso -2Baniso -3
1--0.223 Å2-0.672 Å20 Å2
2---0.223 Å20 Å2
3---0.447 Å2
Refinement stepCycle: LAST / Resolution: 1.8→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1306 0 12 186 1504
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.9461.5
X-RAY DIFFRACTIONc_scbond_it2.7972
X-RAY DIFFRACTIONc_mcangle_it2.7392
X-RAY DIFFRACTIONc_scangle_it4.0552.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
1.8-1.830.255560.209897953
1.83-1.870.228520.211936988
1.87-1.910.316430.189914957
1.91-1.950.225510.175922973
1.95-1.990.27500.188927977
1.99-2.040.244550.189905960
2.04-2.10.219470.19921968
2.1-2.160.189570.17937994
2.16-2.230.168620.166911973
2.23-2.310.214540.166925979
2.31-2.40.229380.185931969
2.4-2.510.191500.18932982
2.51-2.640.208580.177925983
2.64-2.810.233470.1799561003
2.81-3.030.228510.201924975
3.03-3.330.235410.199671008
3.33-3.810.197480.167944992
3.81-4.80.22560.1679671023
4.8-500.010.219540.2310221076
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION3slb.par

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