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- PDB-1t97: Use of sequence duplication to engineer a ligand-triggered long-d... -

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Basic information

Entry
Database: PDB / ID: 1t97
TitleUse of sequence duplication to engineer a ligand-triggered long-distance molecular switch in T4 Lysozyme
ComponentsLysozyme
KeywordsHYDROLASE / MOLECULAR SWITCH / T4 LYSOZYME / NANO-BIOTECHNOLOGY / PROTEIN ENGINEERING / PROTEIN DESIGN / SEQUENCE DUPLICATION
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
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsYousef, M.S. / Baase, W.A. / Matthews, B.W.
Citation
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.
#1: 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.
#2: Journal: Plant Mol.Biol. / Year: 2003
Title: Long-distance conformational changes in a protein engineered by modulated sequence duplication.
Authors: Sagermann, M. / Gay, L. / Matthews, B.W.
History
DepositionMay 14, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 19, 2018Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.4Oct 27, 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 1.5Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysozyme
B: Lysozyme


Theoretical massNumber of molelcules
Total (without water)39,3712
Polymers39,3712
Non-polymers00
Water1,47782
1
A: Lysozyme


Theoretical massNumber of molelcules
Total (without water)19,6861
Polymers19,6861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lysozyme


Theoretical massNumber of molelcules
Total (without water)19,6861
Polymers19,6861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.947, 54.213, 57.983
Angle α, β, γ (deg.)90.00, 103.88, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 19685.541 Da / Num. of mol.: 2
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 2.19 Å3/Da / Density % sol: 43.7 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 30% POLY-ETHYLENE GLYCOL 3400, 100MM HEPES BUFFER, 200MM AMMONIUM ACETATE, pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 11359 / % possible obs: 99 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 36.7 Å2 / Rsym value: 0.067 / Net I/σ(I): 16
Reflection shellResolution: 2.7→2.8 Å / Mean I/σ(I) obs: 7 / Rsym value: 0.15 / % possible all: 99

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→30 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 420103.65 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: FOR MONOMER "A", THERE WAS NO VISIBLE DENSITY FOR RESIDUES 54-61 THERFORE THEY WERE NOT MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.29 484 5.4 %RANDOM
Rwork0.235 ---
obs0.235 8927 98.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.6322 Å2 / ksol: 0.331785 e/Å3
Displacement parametersBiso mean: 38 Å2
Baniso -1Baniso -2Baniso -3
1-6.25 Å20 Å21.57 Å2
2--3.11 Å20 Å2
3----9.36 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.43 Å
Luzzati d res low-5 Å
Luzzati sigma a0.74 Å0.57 Å
Refinement stepCycle: LAST / Resolution: 2.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2670 0 0 82 2752
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.3
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_d0.7
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it5.331.5
X-RAY DIFFRACTIONc_mcangle_it82
X-RAY DIFFRACTIONc_scbond_it8.272
X-RAY DIFFRACTIONc_scangle_it11.282.5
LS refinement shellResolution: 2.7→2.9 Å / Total num. of bins used: 6 /
RfactorNum. reflection
Rwork0.291 0
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAM
X-RAY DIFFRACTION5ION.TOP

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