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- PDB-1p5c: Circular permutation of Helix A in T4 lysozyme -

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Basic information

Entry
Database: PDB / ID: 1p5c
TitleCircular permutation of Helix A in T4 lysozyme
ComponentsLysozyme
KeywordsHYDROLASE / Circular permutation / protein design / context dependent folding
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: 2.5 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

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Assembly

Deposited unit
A: Lysozyme
B: Lysozyme
C: Lysozyme
D: Lysozyme


Theoretical massNumber of molelcules
Total (without water)75,4464
Polymers75,4464
Non-polymers00
Water5,152286
1
A: Lysozyme


Theoretical massNumber of molelcules
Total (without water)18,8621
Polymers18,8621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lysozyme


Theoretical massNumber of molelcules
Total (without water)18,8621
Polymers18,8621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Lysozyme


Theoretical massNumber of molelcules
Total (without water)18,8621
Polymers18,8621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Lysozyme


Theoretical massNumber of molelcules
Total (without water)18,8621
Polymers18,8621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.758, 67.763, 94.057
Angle α, β, γ (deg.)90.00, 92.58, 90.00
Int Tables number4
Space group name H-MP1211
DetailsProtein is a monomer in solution. The asymmetric unit contains 4 molecules. The refinement was performed in the absence of NCS operators.

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Components

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


Mass: 18861.607 Da / Num. of mol.: 4 / Mutation: C54T, C97A, G12M
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 E / Plasmid: phs1403 / Production host: Escherichia coli (E. coli) / Strain (production host): RR1 / References: UniProt: P00720, lysozyme
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / 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: 2.27 Å3/Da / Density % sol: 45.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: 30% PEG 3400, 50mM Phosphate buffer, 5% isopropanol, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 170 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.9537 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 7, 2002 / Details: mirror
RadiationMonochromator: single SI crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.5→25 Å / Num. all: 57195 / Num. obs: 22893 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 35.11 Å2 / Rsym value: 0.076 / Net I/σ(I): 6.7
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 2.4 % / Num. unique all: 3389 / Rsym value: 0.088 / % possible all: 99.3

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Processing

Software
NameVersionClassification
TNTrefinement
SCALAdata scaling
AMoREphasing
CNSrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2LZM

2lzm


Resolution: 2.5→25 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Amino terminal Methionine residue not visible in density.
RfactorNum. reflection% reflectionSelection details
Rfree0.31 2324 -random
Rwork0.248 ---
all0.252 23573 --
obs0.248 22881 97.1 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-6.949 Å20 Å2-1.093 Å2
2---0.106 Å20 Å2
3----6.843 Å2
Refinement stepCycle: LAST / Resolution: 2.5→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5264 0 0 286 5550
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.012
X-RAY DIFFRACTIONt_dihedral_angle_d1.7
X-RAY DIFFRACTIONt_angle_deg13.6

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