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- PDB-1c62: T4 LYSOZYME MUTANT C54T/C97A/F153A IN THE PRESENCE OF 8 ATM XENON -

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Basic information

Entry
Database: PDB / ID: 1c62
TitleT4 LYSOZYME MUTANT C54T/C97A/F153A IN THE PRESENCE OF 8 ATM XENON
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 / XENON / Endolysin
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / Resolution: 2.3 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: Science / Year: 1992
Title: Response of a Protein Structure to Cavity-Creating Mutations and its Relation 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.
#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_conn ...database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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)18,9646
Polymers18,5521
Non-polymers4125
Water1,60389
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.252, 61.252, 97.014
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: 18552.268 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-XE / XENON


Mass: 131.293 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Xe
#4: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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
Crystal grow
*PLUS
pH: 6.7 / Method: batch method / Details: Remington, S.J., (1978) J.Mol.Biol., 118, 81.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein11
20.55 M11NaCl
314 mMmercaptoethanol11
41 mM11MgCl2
50.01 Msodium phosphate11
62.2 M11NaH2PO4
71.8 M11K2HPO4

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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: Oct 2, 1996
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→60 Å / Num. obs: 9602 / % possible obs: 97.5 % / Observed criterion σ(I): 0 / Redundancy: 3.45 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 7
Reflection shellResolution: 2.3→2.34 Å / Rmerge(I) obs: 0.294 / % possible all: 96.3
Reflection
*PLUS
% possible obs: 97 %
Reflection shell
*PLUS
% possible obs: 96.3 %

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Processing

Software
NameClassification
TNTrefinement
DENZOdata reduction
SCALEPACKdata scaling
TNTphasing
RefinementStarting model: 1L85

1l85


Resolution: 2.3→60 Å / Isotropic thermal model: TNT BCORREL / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
RfactorNum. reflection% reflection
all0.171 9989 -
obs-9989 97.5 %
Solvent computationSolvent model: MOEWS AND KRETSINGER / Bsol: 298 Å2 / ksol: 0.897 e/Å3
Refinement stepCycle: LAST / Resolution: 2.3→60 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1286 0 8 89 1383
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01913090.8
X-RAY DIFFRACTIONt_angle_deg2.86117591.3
X-RAY DIFFRACTIONt_dihedral_angle_d15.828020
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.013342
X-RAY DIFFRACTIONt_gen_planes0.0151885
X-RAY DIFFRACTIONt_it4.89813091
X-RAY DIFFRACTIONt_nbd0.0311210
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg15.820
X-RAY DIFFRACTIONt_plane_restr0.0155

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