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- PDB-2f47: Xray crystal structure of T4 lysozyme mutant L20/R63A liganded to... -

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Basic information

Entry
Database: PDB / ID: 2f47
TitleXray crystal structure of T4 lysozyme mutant L20/R63A liganded to methylguanidinium
ComponentsLysozyme
KeywordsHYDROLASE / MOLECULAR SWITCH / T4 LYSOZYME / NANO-BITECHNOLOGY / PROTEIN ENGINEERING / PROTEIN DESIGN
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
BETA-MERCAPTOETHANOL / 1-METHYLGUANIDINE / Endolysin
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsYousef, M.S. / Bischoff, N. / Dyer, C.M. / Baase, W.A. / Matthews, B.W.
Citation
Journal: Protein Sci. / Year: 2006
Title: Guanidinium derivatives bind preferentially and trigger long-distance conformational changes in an engineered T4 lysozyme.
Authors: Yousef, M.S. / Bischoff, N. / Dyer, C.M. / Baase, W.A. / Matthews, B.W.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2004
Title: Use of Sequence Duplication to Engineer a Ligand-Triggered, Long-Distance Molecular Switch in T4 Lysozyme.
Authors: Yousef, M.S. / Baase, W.A. / Matthews, B.W.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1999
Title: Structural Characterization of an Engineered Tandem Repeat Contrasts the Importance of Context and Sequence in Protein Folding.
Authors: Sagermann, M. / Baase, W.A. / Matthews, B.W.
#3: Journal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: Long-Distance Conformational Changes in a Protein Engineered by Modulated Sequence Duplication
Authors: Sagermann, M. / Gay, L. / Matthews, B.W.
History
DepositionNov 22, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Oct 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 1.5Aug 23, 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)19,8724
Polymers19,6861
Non-polymers1873
Water3,297183
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.685, 60.685, 95.482
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: 19685.541 Da / Num. of mol.: 1 / Mutation: L39I, INS (NAAKSELDKAI -N62), R63A, C65T, C108A
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 / Production host: Escherichia coli (E. coli) / References: UniProt: P00720, lysozyme
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-MGX / 1-METHYLGUANIDINE


Mass: 73.097 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H7N3
#4: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.8 M MIXED POTASSIUM AND SODIUM PHOSPHATE. 0.2 M GUANIDINIUM CHLORIDE, pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. obs: 22811 / % possible obs: 99 % / Biso Wilson estimate: 22.8 Å2 / Rsym value: 0.087 / Net I/σ(I): 36
Reflection shellResolution: 1.7→1.76 Å / Mean I/σ(I) obs: 8 / Rsym value: 0.222 / % possible all: 100

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Processing

Software
NameVersionClassification
DENZODENZOdata reduction
SCALEPACKDENZOdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1T8A

1t8a


Resolution: 1.7→30 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 750281.6817 / Data cutoff high rms absF: 750281.6817 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.217 1097 5 %RANDOM
Rwork0.206 ---
all0.21 ---
obs0.206 22555 99 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.7917 Å2 / ksol: 0.397234 e/Å3
Displacement parametersBiso mean: 25 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20.62 Å20 Å2
2---0.08 Å20 Å2
3---0.17 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.06 Å
Refinement stepCycle: LAST / Resolution: 1.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1382 0 15 183 1580
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.87
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.371.5
X-RAY DIFFRACTIONc_mcangle_it2.172
X-RAY DIFFRACTIONc_scbond_it2.272
X-RAY DIFFRACTIONc_scangle_it3.442.5
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.266 173 4.9 %
Rwork0.226 3335 -
obs--94 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3mgn.parammgn.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5BME.paramBME.top

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