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- PDB-1l48: STRUCTURAL AND THERMODYNAMIC ANALYSIS OF THE PACKING OF TWO ALPHA... -

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Entry
Database: PDB / ID: 1l48
TitleSTRUCTURAL AND THERMODYNAMIC ANALYSIS OF THE PACKING OF TWO ALPHA-HELICES IN BACTERIOPHAGE T4 LYSOZYME
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: 1.7 Å
AuthorsDaopin, S. / Matthews, B.W.
Citation
Journal: J.Mol.Biol. / Year: 1991
Title: Structural and thermodynamic analysis of the packing of two alpha-helices in bacteriophage T4 lysozyme.
Authors: Daopin, S. / Alber, T. / Baase, W.A. / Wozniak, J.A. / Matthews, B.W.
#2: Journal: To be Published
Title: The Structural and Thermodynamic Consequences of Burying a Charged Residue within the Hydrophobic Core of T4 Lysozyme
Authors: Daopin, S. / Anderson, E. / Baase, W. / Dahlquist, F.W. / Matthews, B.W.
#3: Journal: To be Published
Title: Multiple Stabilizing Alanine Replacements within Alpha-Helix 126-134 of T4 Lysozyme Have Independent, Additive Effects on Both Structure and Stability
Authors: Zhang, X.-J. / Baase, W.A. / Matthews, B.W.
#4: Journal: To be Published
Title: Tolerance of T4 Lysozyme to Proline Substitutions within the Long Interdomain Alpha-Helix Illustrates the Adaptability of Proteins to Potentially Destabilizing Lesions
Authors: Sauer, U.H. / Dao-Pin, S. / Matthews, B.W.
#5: Journal: To be Published
Title: Tolerance of T4 Lysozyme to Multiple Xaa (Right Arrow) Ala Substitutions: A Polyalanine Alpha-Helix Containing Ten Consecutive Alanines
Authors: Heinz, D.W. / Baase, W.A. / Matthews, B.W.
#6: Journal: J.Mol.Biol. / Year: 1991
Title: Cumulative Site-Directed Charge-Change Replacements in Bacteriophage T4 Lysozyme Suggest that Long-Range Electrostatic Interactions Contribute Little to Protein Stability
Authors: Dao-Pin, S. / Soderlind, E. / Baase, W.A. / Wozniak, J.A. / Sauer, U. / Matthews, B.W.
#7: Journal: Biochemistry / Year: 1991
Title: Analysis of the Interaction between Charged Side Chains and the Alpha-Helix Dipole Using Designed Thermostable Mutants of Phage T4 Lysozyme
Authors: Nicholson, H. / Anderson, D.E. / Dao-Pin, S. / Matthews, B.W.
#8: Journal: Biochemistry / Year: 1991
Title: Contributions of Engineered Surface Salt Bridges to the Stability of T4 Lysozyme Determined by Directed Mutagenesis
Authors: Dao-Pin, S. / Sauer, U. / Nicholson, H. / Matthews, B.W.
#9: Journal: Biochemistry / Year: 1991
Title: Toward a Simplification of the Protein Folding Problem: A Stabilizing Polyalanine Alpha-Helix Engineered in T4 Lysozyme
Authors: Zhang, X.-J. / Baase, W.A. / Matthews, B.W.
#10: Journal: Biochemistry / Year: 1990
Title: Structure of a Thermostable Disulfide-Bridge Mutant of Phage T4 Lysozyme Shows that an Engineered Crosslink in a Flexible Region Does not Increase the Rigidity of the Folded Protein
Authors: Pjura, P.E. / Matsumura, M. / Wozniak, J.A. / Matthews, B.W.
#11: Journal: J.Biol.Chem. / Year: 1989
Title: Structural Studies of Mutants of T4 Lysozyme that Alter Hydrophobic Stabilization
Authors: Matsumura, M. / Wozniak, J.A. / Dao-Pin, S. / Matthews, B.W.
#12: Journal: Biochemistry / Year: 1989
Title: High-Resolution Structure of the Temperature-Sensitive Mutant of Phage Lysozyme, Arg 96 (Right Arrow) His
Authors: Weaver, L.H. / Gray, T.M. / Gruetter, M.G. / Anderson, D.E. / Wozniak, J.A. / Dahlquist, F.W. / Matthews, B.W.
#13: Journal: J.Mol.Biol. / Year: 1989
Title: Contributions of Left-Handed Helical Residues to the Structure and Stability of Bacteriophage T4 Lysozyme
Authors: Nicholson, H. / Soderlind, E. / Tronrud, D.E. / Matthews, B.W.
#14: Journal: Nature / Year: 1988
Title: Hydrophobic Stabilization in T4 Lysozyme Determined Directly by Multiple Substitutions of Ile 3
Authors: Matsumura, M. / Becktel, W.J. / Matthews, B.W.
#15: Journal: Nature / Year: 1988
Title: Enhanced Protein Thermostability from Designed Mutations that Interact with Alpha-Helix Dipoles
Authors: Nicholson, H. / Becktel, W.J. / Matthews, B.W.
#16: Journal: Science / Year: 1988
Title: Replacements of Pro86 in Phage T4 Lysozyme Extend an Alpha-Helix But Do not Alter Protein Stability
Authors: Alber, T. / Bell, J.A. / Dao-Pin, S. / Nicholson, H. / Wozniak, J.A. / Cook, S. / Matthews, B.W.
#17: Journal: Proc.Natl.Acad.Sci.USA / Year: 1987
Title: Enhanced Protein Thermostability from Site-Directed Mutations that Decrease the Entropy of Unfolding
Authors: Matthews, B.W. / Nicholson, H. / Becktel, W.J.
#18: Journal: J.Biol.Chem. / Year: 1987
Title: Structural Analysis of the Temperature-Sensitive Mutant of Bacteriophage T4 Lysozyme, Glycine 156 (Right Arrow) Aspartic Acid
Authors: Gray, T.M. / Matthews, B.W.
#19: Journal: Nature / Year: 1987
Title: Contributions of Hydrogen Bonds of Thr 157 to the Thermodynamic Stability of Phage T4 Lysozyme
Authors: Alber, T. / Dao-Pin, S. / Wilson, K. / Wozniak, J.A. / Cook, S.P. / Matthews, B.W.
#20: Journal: J.Mol.Biol. / Year: 1987
Title: Structural Studies of Mutants of the Lysozyme of Bacteriophage T4. The Temperature-Sensitive Mutant Protein Thr157 (Right Arrow) Ile
Authors: Gruetter, M.G. / Gray, T.M. / Weaver, L.H. / Alber, T. / Wilson, K. / Matthews, B.W.
#21: Journal: J.Mol.Biol. / Year: 1987
Title: Structure of Bacteriophage T4 Lysozyme Refined at 1.7 Angstroms Resolution
Authors: Weaver, L.H. / Matthews, B.W.
#22: Journal: Biochemistry / Year: 1987
Title: Temperature-Sensitive Mutations of Bacteriophage T4 Lysozyme Occur at Sites with Low Mobility and Low Solvent Accessibility in the Folded Protein
Authors: Alber, T. / Dao-Pin, S. / Nye, J.A. / Muchmore, D.C. / Matthews, B.W.
#23: Journal: Nature / Year: 1981
Title: Common Precursor of Lysozymes of Hen Egg-White and Bacteriophage T4
Authors: Matthews, B.W. / Gruetter, M.G. / Anderson, W.F. / Remington, S.J.
#24: Journal: J.Mol.Biol. / Year: 1981
Title: Crystallographic Determination of the Mode of Binding of Oligosaccharides to T4 Bacteriophage Lysozyme. Implications for the Mechanism of Catalysis
Authors: Anderson, W.F. / Gruetter, M.G. / Remington, S.J. / Weaver, L.H. / Matthews, B.W.
#25: Journal: J.Mol.Biol. / Year: 1981
Title: Relation between Hen Egg White Lysozyme and Bacteriophage T4 Lysozyme. Evolutionary Implications
Authors: Matthews, B.W. / Remington, S.J. / Gruetter, M.G. / Anderson, W.F.
#26: Journal: J.Mol.Biol. / Year: 1978
Title: Structure of the Lysozyme from Bacteriophage T4, an Electron Density Map at 2.4 Angstroms Resolution
Authors: Remington, S.J. / Anderson, W.F. / Owen, J. / Teneyck, L.F. / Grainger, C.T. / Matthews, B.W.
#27: Journal: Biochem.Biophys.Res.Commun. / Year: 1977
Title: Atomic Coordinates for T4 Phage Lysozyme
Authors: Remington, S.J. / Teneyck, L.F. / Matthews, B.W.
#28: Journal: Biochim.Biophys.Acta / Year: 1975
Title: Comparison of the Predicted and Observed Secondary Structure of T4 Phage Lysozyme
Authors: Matthews, B.W.
#29: Journal: Proc.Natl.Acad.Sci.USA / Year: 1974
Title: The Three Dimensional Structure of the Lysozyme from Bacteriophage T4
Authors: Matthews, B.W. / Remington, S.J.
#30: Journal: J.Mol.Biol. / Year: 1973
Title: Crystallographic Data for Lysozyme from Bacteriophage T4
Authors: Matthews, B.W. / Dahlquist, F.W. / Maynard, A.Y.
#1: Journal: To be Published
Authors: Nicholson, H. / Becktel, W. / Matthews, B.W.
History
DepositionJan 28, 1991Processing site: BNL
Revision 1.0Oct 15, 1991Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 2.0Nov 23, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Source and taxonomy
Category: atom_site / atom_sites ...atom_site / atom_sites / citation_author / database_2 / database_PDB_matrix / entity_src_gen / pdbx_database_remark / pdbx_validate_rmsd_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[1][2] / _atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[2][2] / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _database_PDB_matrix.origx[1][1] / _database_PDB_matrix.origx[1][2] / _database_PDB_matrix.origx[2][1] / _database_PDB_matrix.origx[2][2] / _entity_src_gen.pdbx_gene_src_organ / _pdbx_validate_rmsd_angle.angle_deviation / _pdbx_validate_rmsd_angle.angle_value / _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
Details: ORTHOGONAL X,Y,Z AXES WERE REALIGNED FROM A*,B,C TO A,B*,C CRYSTALLOGRAPHIC DIRECTIONS
Provider: repository / Type: Remediation
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 CITED AS REFERENCE 26 ABOVE 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)18,7692
Polymers18,6911
Non-polymers781
Water2,666148
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, 96.800
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Atom site foot note1: RESIDUES 162 - 164 IN WILD-TYPE AND ALL MUTANT LYSOZYMES ARE EXTREMELY MOBILE. THUS THE COORDINATES FOR THESE RESIDUES ARE VERY UNRELIABLE.
2: SG SEO 97 IS BONDED TO SG CYS 97.

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Components

#1: Protein T4 LYSOZYME


Mass: 18690.521 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.: 148 / 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: 2.8 Å3/Da / Density % sol: 56.06 %
Crystal grow
*PLUS
pH: 6.7 / Method: batch method
Details: taken from Remington, S.J. et al (1978). J. Mol. Biol., 81-98.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein11
20.55 M11NaCl
314 mMmercaptoethanol11
41 mM11MgCl2
50.01 Msodium phospahte11
62.2 M11NaH2PO4
71.8 M11K2HPO4

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Num. obs: 15215 / Num. measured all: 23731 / Rmerge(I) obs: 0.058

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Processing

SoftwareName: TNT / Classification: refinement
RefinementResolution: 1.7→6 Å / Rfactor obs: 0.166
Details: RESIDUES 162 - 164 IN WILD-TYPE AND ALL MUTANT LYSOZYMES ARE EXTREMELY MOBILE. THUS THE COORDINATES FOR THESE RESIDUES ARE VERY UNRELIABLE.
Refinement stepCycle: LAST / Resolution: 1.7→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1311 0 4 148 1463
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.018
X-RAY DIFFRACTIONt_angle_deg2.7
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: 1.7 Å / Lowest resolution: 6 Å / Num. reflection obs: 14641 / Rfactor obs: 0.166
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_d2.7
X-RAY DIFFRACTIONt_angle_deg2.8
X-RAY DIFFRACTIONt_plane_restr0.017

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