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- PDB-1p56: Duplication-extension of Helix A of T4 lysozyme -

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Basic information

Entry
Database: PDB / ID: 1p56
TitleDuplication-extension of Helix A of T4 lysozyme
ComponentsPROTEIN (Lysozyme)
KeywordsHYDROLASE / sequence duplication / folding propensity / completion folding experiment
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
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSagermann, M. / Gay, L. / Baase, W.A. / Matthews, B.W.
Citation
Journal: Biochemistry / Year: 2004
Title: Relocation or duplication of the helix A sequence of T4 lysozyme causes only modest changes in structure but can increase or decrease the rate of folding.
Authors: Sagermann, M. / Baase, W.A. / Mooers, B.H. / Gay, L. / Matthews, B.W.
#1: Journal: J.Mol.Biol. / Year: 2002
Title: Crystal structures of a T4-lysozyme duplication-extension mutant demonstrates that the highly conserved beta-sheet region has low intrinsic folding propensity
Authors: Sagermann, M. / Matthews, B.W.
#2: Journal: J.Mol.Biol. / Year: 1987
Title: Structure of bacteriophage T4 lysozyme refined at 1.7 A resolution
Authors: Weaver, L.H. / Matthews, B.W.
#3: 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.
History
DepositionApr 25, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Aug 14, 2019Group: Data collection / Category: computing
Revision 1.5Oct 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 1.6Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 999SEQUENCE Residue Leu 164 was deleted and sequence SGGAMNIFEMLRIDE was appended to the C-terminus

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (Lysozyme)


Theoretical massNumber of molelcules
Total (without water)19,9541
Polymers19,9541
Non-polymers00
Water2,162120
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.300, 60.300, 96.396
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 PROTEIN (Lysozyme) / Lysis protein / Muramidase / Endolysin


Mass: 19953.857 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: Gene product E / Plasmid: phs1403 / Production host: Escherichia coli (E. coli) / Strain (production host): RR1 / References: UniProt: P00720, lysozyme
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 2.75 Å3/Da / Density % sol: 55.25 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 35% PEG 4000, 50mM phosphate buffer, 5% isopropanol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 170 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.999 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 10, 2002 / Details: mirrors
RadiationMonochromator: Flat mirror, single SI crystal bend / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 1.7→28.75 Å / Num. obs: 22444 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 14.24 Å2 / Rsym value: 0.066 / Net I/σ(I): 7.2
Reflection shellResolution: 1.79→1.9 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 5.1 / Num. unique all: 3053 / Rsym value: 0.11 / % possible all: 98.7

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Processing

Software
NameClassification
TNTrefinement
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2LZM

2lzm


Resolution: 1.8→30 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Only disconnected density could be seen in the vicinity of the old c-terminus. Therefore, the sequence of the appended residues SGGAMNIFEMLRIDE could not be placed reliably into the density ...Details: Only disconnected density could be seen in the vicinity of the old c-terminus. Therefore, the sequence of the appended residues SGGAMNIFEMLRIDE could not be placed reliably into the density and was omitted in the final model.
RfactorNum. reflectionSelection details
Rfree0.273 1926 random
Rwork0.208 --
all0.215 19144 -
obs0.214 17218 -
Displacement parametersBiso mean: 0.74 Å2
Baniso -1Baniso -2Baniso -3
1-0.74 Å20.68 Å20 Å2
2--0.74 Å20 Å2
3----1.48 Å2
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1292 0 0 120 1412
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.014
X-RAY DIFFRACTIONt_dihedral_angle_d1.777
X-RAY DIFFRACTIONt_angle_deg13.607

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