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- PDB-2o79: T4 lysozyme with C-terminal extension -

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Basic information

Entry
Database: PDB / ID: 2o79
TitleT4 lysozyme with C-terminal extension
ComponentsLysozyme
KeywordsHYDROLASE / PROTEIN STABILITY / PROTEIN FOLDING / LYSOZYME / CIRCULAR PERMUTANT
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 / Phage lysozyme / Lysozyme domain superfamily / Lysozyme / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATE ION / Endolysin
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLlinas, M. / Crowder, S.M. / Echols, N. / Alber, T. / Marqusee, S.
CitationJournal: Protein Sci. / Year: 2007
Title: Exploring subdomain cooperativity in T4 lysozyme I: Structural and energetic studies of a circular permutant and protein fragment.
Authors: Cellitti, J. / Llinas, M. / Echols, N. / Shank, E.A. / Gillespie, B. / Kwon, E. / Crowder, S.M. / Dahlquist, F.W. / Alber, T. / Marqusee, S.
History
DepositionDec 10, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 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

Downloads & links

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Assembly

Deposited unit
A: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3096
Polymers19,0161
Non-polymers2935
Water4,486249
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.117, 60.117, 97.108
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-615-

HOH

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Components

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


Mass: 19015.711 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 / Plasmid: pET27K / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta/pLacI / References: UniProt: P00720, lysozyme
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / 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: 2.66 Å3/Da / Density % sol: 53.82 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 0.9 M K2HPO4, 1.1 M NaH2PO4, pH 6.6, 0.25 M NaCl, 49.0 mM oxidized B mercaptoethanol, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jun 1, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. all: 19210 / Num. obs: 19210 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Biso Wilson estimate: 14.76 Å2 / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 52.7
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.214 / Mean I/σ(I) obs: 14.5 / Num. unique all: 1760 / Rsym value: 0.214 / % possible all: 92

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1sx7

1sx7


Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.938 / SU B: 1.668 / SU ML: 0.055 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.1 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18173 964 5.1 %RANDOM
Rwork0.14845 ---
all0.15013 18987 --
obs0.15013 18987 97.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 11.308 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20.09 Å20 Å2
2--0.17 Å20 Å2
3----0.26 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1282 0 14 249 1545
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221346
X-RAY DIFFRACTIONr_bond_other_d0.0010.021239
X-RAY DIFFRACTIONr_angle_refined_deg1.2841.9561821
X-RAY DIFFRACTIONr_angle_other_deg0.80432867
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9985169
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.20323.59464
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.94415242
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.671513
X-RAY DIFFRACTIONr_chiral_restr0.0710.2201
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021514
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02284
X-RAY DIFFRACTIONr_nbd_refined0.2310.2301
X-RAY DIFFRACTIONr_nbd_other0.1830.21226
X-RAY DIFFRACTIONr_nbtor_refined0.1780.2675
X-RAY DIFFRACTIONr_nbtor_other0.0810.2750
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2560.2173
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1910.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2840.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1770.222
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0531.5899
X-RAY DIFFRACTIONr_mcbond_other0.2461.5342
X-RAY DIFFRACTIONr_mcangle_it1.32121327
X-RAY DIFFRACTIONr_scbond_it2.483578
X-RAY DIFFRACTIONr_scangle_it3.6544.5494
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.897 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.194 133 -
Rwork0.154 2482 -
obs-2615 94.75 %

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