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- PDB-1l99: PERTURBATION OF TRP 138 IN T4 LYSOZYME BY MUTATIONS AT GLN 105 US... -

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Basic information

Entry
Database: PDB / ID: 1l99
TitlePERTURBATION OF TRP 138 IN T4 LYSOZYME BY MUTATIONS AT GLN 105 USED TO CORRELATE CHANGES IN STRUCTURE, STABILITY, SOLVATION, AND SPECTROSCOPIC PROPERTIES
ComponentsT4 LYSOZYME
KeywordsHYDROLASE(O-GLYCOSYL)
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: 1.95 Å
AuthorsPjura, P. / Mcintosh, L.P. / Wozniak, J.A. / Matthews, B.W.
CitationJournal: Proteins / Year: 1993
Title: Perturbation of Trp 138 in T4 lysozyme by mutations at Gln 105 used to correlate changes in structure, stability, solvation, and spectroscopic properties.
Authors: Pjura, P. / McIntosh, L.P. / Wozniak, J.A. / Matthews, B.W.
History
DepositionJul 13, 1992Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.process_site / _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
Remark 700SHEET THERE ARE SEVERAL SUBTLE ASPECTS OF THE SECONDARY STRUCTURE OF THIS MOLECULE WHICH CANNOT ...SHEET THERE ARE SEVERAL SUBTLE ASPECTS OF THE SECONDARY STRUCTURE OF THIS MOLECULE WHICH CANNOT CONVENIENTLY BE REPRESENTED IN THE HELIX AND SHEET RECORDS BELOW. THESE ASPECTS INFLUENCE THE REPRESENTATION OF HELIX 6 AND STRAND 3 OF SHEET *S1*. THE PAPER J.MOL.BIOL., V. 118, P. 81, 1978 SHOULD BE CONSULTED FOR THESE SUBTLETIES.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: T4 LYSOZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6702
Polymers18,5911
Non-polymers781
Water2,414134
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.200, 61.200, 95.600
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Atom site foot note1: SG SEO 97 IS BONDED TO SG CYS 97.
2: RESIDUES 162 - 164 IN WILD-TYPE AND ALL MUTANT LYSOZYMES ARE EXTREMELY MOBILE. THUS THE COORDINATES FOR THESE RESIDUES ARE VERY UNRELIABLE.

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Components

#1: Protein T4 LYSOZYME


Mass: 18591.391 Da / Num. of mol.: 1
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 / Plasmid: M13 / References: UniProt: P00720, lysozyme
#2: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


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


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.78 Å3/Da / Density % sol: 55.75 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6.5 / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
115 mg/mlprotein11
20.1 M11or KPO4Na
30.55 M11NaCl
40.02 %11NaN3
51.6-2.2 Mphosphate11

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Num. obs: 11881 / Num. measured all: 27921 / Rmerge(I) obs: 0.092

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Processing

SoftwareName: TNT / Classification: refinement
RefinementRfactor obs: 0.168 / Highest resolution: 1.95 Å
Details: RESIDUES 162 - 164 IN WILD-TYPE AND ALL MUTANT LYSOZYMES ARE EXTREMELY MOBILE. THUS THE COORDINATES FOR THESE RESIDUES ARE VERY UNRELIABLE. THE SIDE CHAINS OF RESIDUES 8, 13, 14, 76, 80, AND ...Details: RESIDUES 162 - 164 IN WILD-TYPE AND ALL MUTANT LYSOZYMES ARE EXTREMELY MOBILE. THUS THE COORDINATES FOR THESE RESIDUES ARE VERY UNRELIABLE. THE SIDE CHAINS OF RESIDUES 8, 13, 14, 76, 80, AND 119 HAVE WEAK DENSITY AND PROBABLY ARE IN MULTIPLE CONFORMATIONS. THE SIDE CHAINS OF RESIDUES 16, 55, 83, AND 162 HAVE VERY WEAK OR NONEXISTENT DENSITY AND THE MODELS FOR THESE SIDE CHAINS SHOULD NOT BE CONSIDERED RELIABLE.
Refinement stepCycle: LAST / Highest resolution: 1.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1304 0 4 134 1442
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.016
X-RAY DIFFRACTIONt_angle_deg2.9
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
Refinement
*PLUS
Highest resolution: 1.95 Å / Lowest resolution: 6 Å / Num. reflection obs: 11226 / Rfactor obs: 0.168
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONt_angle_d
X-RAY DIFFRACTIONt_angle_deg

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