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- PDB-1jtm: Alternative Structures of a Sequence Extended T4 Lysozyme Show th... -

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Basic information

Entry
Database: PDB / ID: 1jtm
TitleAlternative Structures of a Sequence Extended T4 Lysozyme Show that the Highly Conserved Beta-Sheet has Weak Intrinsic Folding Propensity
ComponentsLYSOZYME
KeywordsHYDROLASE / SEQUENCE DUPLICATION / CONTEXT DEPENDENT FOLDING / SEQUENCE REPEAT
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 / Endolysin
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsSagermann, M. / Matthews, B.W.
Citation
Journal: J.Mol.Biol. / Year: 2002
Title: Crystal Structures of a T4-lysozyme Duplication-extension Mutant Demonstrate that the Highly Conserved beta-Sheet Region has Low Intrinsic Folding Propensity
Authors: Sagermann, M. / 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: J.Mol.Biol. / Year: 1987
Title: Structure of Bacteriophage T4 Lysozyme Refined at 1.7 A Resolution
Authors: Weaver, L.H. / Matthews, B.W.
History
DepositionAug 21, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Oct 27, 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 16, 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)20,2992
Polymers20,2211
Non-polymers781
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.970, 60.970, 97.345
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


Mass: 20221.203 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: E / Plasmid: PHS1403 / Production host: Escherichia coli (E. coli) / Strain (production host): RR1 / References: UniProt: P00720, lysozyme
#2: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS

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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 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 50MM TRIS-GLYCINE, 20% PEG 8000, 10% Isopropanol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 7.5 / Details: used microseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
150 mMTris-glycine1droppH7.5
2100 mM1dropNaCl
320 mg/mlprotein1drop
420 %(w/v)PEG80001reservoir
510 %(v/v)isopropanol1reservoir
650 mMphosphate1reservoirpH7.0

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Data collection

DiffractionMean temperature: 170 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 21, 1999 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→17 Å / Num. all: 19736 / Num. obs: 19736 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 24.7 Å2 / Rsym value: 0.069 / Net I/σ(I): 3.9
Reflection shellResolution: 1.9→2.01 Å / Redundancy: 4 % / Mean I/σ(I) obs: 2.6 / Num. unique all: 2714 / Rsym value: 0.26 / % possible all: 99.8
Reflection
*PLUS
Rmerge(I) obs: 0.068

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Processing

Software
NameVersionClassification
TNTrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementStarting model: PDB ID 2LZM

2lzm


Resolution: 1.9→17 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: The structure was refined in the absence of water molecules. Only a BME molecule and a polyalanine peptide chain was fitted into difference density. The inserted polyalanine refined to a ...Details: The structure was refined in the absence of water molecules. Only a BME molecule and a polyalanine peptide chain was fitted into difference density. The inserted polyalanine refined to a grouped occupancy of ca. 0.3. Other less clear difference densities were observed as well but not fitted. The fitted chain was labeled with chain B. The connection of this chain to the c-terminus of the molecule is in very weak density and was not modeled.The former c-terminal residues Asn163 and Leu164 could were not detectable as well. Combination of CNS, BUSTER and TNT used for refinement.
RfactorNum. reflectionSelection details
Rfree0.265 1297 random
Rwork0.214 --
all0.219 16545 -
obs0.219 16545 -
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.49 Å20.49 Å20 Å2
2--0.49 Å20 Å2
3----0.98 Å2
Refinement stepCycle: LAST / Resolution: 1.9→17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1338 0 4 0 1342
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.01
X-RAY DIFFRACTIONt_angle_deg1.38
Refinement
*PLUS
Highest resolution: 1.9 Å / Rfactor all: 0.219 / Rfactor obs: 0.214 / Rfactor Rfree: 0.265 / Rfactor Rwork: 0.214
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: t_angle_deg / Dev ideal: 1.4

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