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- PDB-1cvk: T4 LYSOZYME MUTANT L118A -

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Basic information

Entry
Database: PDB / ID: 1cvk
TitleT4 LYSOZYME MUTANT L118A
ComponentsLYSOZYME
KeywordsHYDROLASE / HYDROLASE (O-GLYCOSYL) / T4 LYSOZYME / CAVITY-FORMING MUTANT / PROTEIN ENGINEERING / PROTEIN 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
2-HYDROXYETHYL DISULFIDE / Endolysin
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsGassner, N.C. / Baase, W.A. / Lindstrom, J. / Lu, J. / Matthews, B.W.
Citation
Journal: Biochemistry / Year: 1999
Title: Methionine and alanine substitutions show that the formation of wild-type-like structure in the carboxy-terminal domain of T4 lysozyme is a rate-limiting step in folding.
Authors: Gassner, N.C. / Baase, W.A. / Lindstrom, J.D. / Lu, J. / Dahlquist, F.W. / Matthews, B.W.
#1: Journal: Protein Sci. / Year: 1998
Title: The Response of T4 Lysozyme to Large-to-Small Substitutions Within the Core and its Relation to the Hydrophobic Effect
Authors: Xu, J. / Baase, W.A. / Baldwin, E. / Matthews, B.W.
#2: Journal: J.Mol.Biol. / Year: 1995
Title: Alanine Scanning Mutagenesis of the Alpha-Helix 115-123 of Phage T4 Lysozyme: Effects on Structure, Stability and the Binding of Solvent
Authors: Blaber, M. / Baase, W.A. / Gassner, N. / Matthews, B.W.
#3: Journal: Science / Year: 1992
Title: Response of a Protein Structure to Cavity-Creating Mutations and its Relationship to the Hydrophobic Effect
Authors: Eriksson, A.E. / Baase, W.A. / Zhang, X.-J. / Heinz, D.W. / Blaber, M. / Baldwin, E.P. / Matthews, B.W.
#4: 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 23, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 1999Provider: 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 / Item: _software.name
Revision 1.4Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Nov 3, 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 1.6Feb 7, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8114
Polymers18,5861
Non-polymers2253
Water2,126118
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.050, 61.050, 96.920
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


Mass: 18586.283 Da / Num. of mol.: 1 / Mutation: C54T, C97A, L118A
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) / References: UniProt: P00720, lysozyme
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-HED / 2-HYDROXYETHYL DISULFIDE


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 2.8 Å3/Da / Density % sol: 56.15 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: NA2PO4, NACL, VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
pH: 6.7 / Method: vapor diffusion / Details: Eriksson, A.E., (1993) J.Mol.Biol., 229, 747. / PH range low: 7.1 / PH range high: 6.3
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
20.25 M1reservoirNaCl
32.0 Mphosphate1reservoir
4beta-mercaptoethanol1reservoir
51
61
71

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: KODAK / Detector: FILM
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. all: 16392 / Num. obs: 16392 / % possible obs: 92.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.26 % / Rmerge(I) obs: 0.06
Reflection
*PLUS

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Processing

Software
NameVersionClassification
TNTrefinement
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
TNTphasing
RefinementResolution: 1.8→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: TNT PROTGEO
RfactorNum. reflection
Rwork0.157 -
all0.157 15172
obs0.157 15172
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1289 0 10 118 1417
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.015
X-RAY DIFFRACTIONt_angle_deg2
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.8 Å / Rfactor Rwork: 0.157
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: t_angle_deg / Dev ideal: 2

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