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- PDB-1c6p: T4 LYSOZYME MUTANT C54T/C97A IN THE PRESENCE OF 8 ATM ARGON -

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Basic information

Entry
Database: PDB / ID: 1c6p
TitleT4 LYSOZYME MUTANT C54T/C97A IN THE PRESENCE OF 8 ATM ARGON
ComponentsPROTEIN (LYSOZYME)
KeywordsHYDROLASE / HYDROLASE (O-GLYCOSYL) / T4 LYSOZYME / NOBLE GAS BINDING
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
AuthorsQuillin, M.L. / Matthews, B.W.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: Size versus polarizability in protein-ligand interactions: binding of noble gases within engineered cavities in phage T4 lysozyme.
Authors: Quillin, M.L. / Breyer, W.A. / Griswold, I.J. / Matthews, B.W.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1989
Title: Stabilization of Phage T4 Lysozyme by Engineered Disulfide Bonds
Authors: Matsumura, M. / Becktel, W.J. / Levitt, 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.
History
DepositionDec 21, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Oct 4, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 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 1.4Aug 9, 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: PROTEIN (LYSOZYME)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8565
Polymers18,6281
Non-polymers2274
Water2,090116
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.951, 60.951, 97.006
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)


Mass: 18628.363 Da / Num. of mol.: 1 / Mutation: YES
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-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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 %
Crystal growDetails: 1.8-2.2 M NAH2/K2HPO4, PH 6.9-7.1, 50 MM BETA-MERCAPTOETHANOL AND/OR 50 MM HYDROXYETHYL DISULFIDE
PH range: 6.9-7

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Data collection

DiffractionMean temperature: 273 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jun 11, 1996
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→60 Å / Num. obs: 15469 / % possible obs: 92.9 % / Observed criterion σ(I): 0 / Redundancy: 2.67 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 12.9
Reflection shellResolution: 1.9→1.93 Å / Rmerge(I) obs: 0.22 / % possible all: 99
Reflection shell
*PLUS
% possible obs: 99 %

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Processing

Software
NameClassification
TNTrefinement
DENZOdata reduction
SCALEPACKdata scaling
TNTphasing
RefinementStarting model: 1L63

1l63


Resolution: 1.9→60 Å / Isotropic thermal model: TNT BCORREL / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
RfactorNum. reflection% reflection
all0.179 16013 -
obs-16013 92.9 %
Solvent computationSolvent model: MOEWS AND KRETSINGER / Bsol: 300.2 Å2 / ksol: 0.947 e/Å3
Refinement stepCycle: LAST / Resolution: 1.9→60 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1292 0 10 116 1418
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01913190.8
X-RAY DIFFRACTIONt_angle_deg2.6517701.3
X-RAY DIFFRACTIONt_dihedral_angle_d15.098040
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.012342
X-RAY DIFFRACTIONt_gen_planes0.0151895
X-RAY DIFFRACTIONt_it3.1413191
X-RAY DIFFRACTIONt_nbd0.0461410
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refine LS restraints
*PLUS
Type: t_plane_restr / Dev ideal: 0.015 / Weight: 5

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