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- PDB-2f2q: High resolution crystal structure of T4 lysozyme mutant L20R63/A ... -

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Basic information

Entry
Database: PDB / ID: 2f2q
TitleHigh resolution crystal structure of T4 lysozyme mutant L20R63/A liganded to guanidinium ion
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 / Lysozyme domain superfamily / Phage lysozyme / Lysozyme / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
GUANIDINE / 2-HYDROXYETHYL DISULFIDE / Endolysin
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 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 17, 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 1.4Dec 19, 2018Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.5Sep 2, 2020Group: Database references / Derived calculations / Structure summary
Category: struct / struct_ref_seq_dif / struct_site
Item: _struct.title / _struct_ref_seq_dif.details ..._struct.title / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.7Aug 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)19,9344
Polymers19,6861
Non-polymers2493
Water3,261181
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.712, 60.712, 95.352
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: I39L, A63R, T65C, A108C
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: pHS1403 / Production host: Escherichia coli (E. coli) / Strain (production host): RR1 cells / References: UniProt: P00720, lysozyme
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 59.070 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH5N3
#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 / Water


Mass: 18.015 Da / Num. of mol.: 181 / 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: 2.64 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 277 K / pH: 6.5
Details: 0.5 mM protein, 1.8 M MIXED POTASSIUM AND SODIUM PHOSPHATE, 0.2 M GUANIDINIUM CHLORIDE, PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K, pH 6.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.953
DetectorType: ADSC / Detector: CCD / Date: May 26, 2005 / Details: KOHZU: Double Crystal Si(111)
RadiationMonochromator: Double crystal, Si(111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953 Å / Relative weight: 1
ReflectionResolution: 1.45→30 Å / Num. obs: 36743 / % possible obs: 90 % / Biso Wilson estimate: 18.7 Å2 / Rsym value: 0.077 / Net I/σ(I): 27
Reflection shellResolution: 1.45→1.5 Å / Mean I/σ(I) obs: 3.6 / Rsym value: 0.228 / % possible all: 89

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Processing

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

1t8a


Resolution: 1.45→30 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1714737.73 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.223 1618 5 %RANDOM
Rwork0.2 ---
obs0.2 32322 90 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.1 Å2 / ksol: 0.39 e/Å3
Displacement parametersBiso mean: 22.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å21.22 Å20 Å2
2--0.48 Å20 Å2
3----0.96 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.18 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.07 Å0.07 Å
Refinement stepCycle: LAST / Resolution: 1.45→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1414 0 13 181 1608
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
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_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.07
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.131.5
X-RAY DIFFRACTIONc_mcangle_it32
X-RAY DIFFRACTIONc_scbond_it4.212
X-RAY DIFFRACTIONc_scangle_it5.542.5
LS refinement shellResolution: 1.45→1.54 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.267 250 4.9 %
Rwork0.227 4809 -
obs--84.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3GAI.PARAMGAI.TOP
X-RAY DIFFRACTION4ION.PARAMBME_OX.TOP
X-RAY DIFFRACTION5BME_OX.PARAMION.TOP

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