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- PDB-1l21: CONTRIBUTIONS OF LEFT-HANDED HELICAL RESIDUES TO THE STRUCTURE AN... -

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Entry
Database: PDB / ID: 1l21
TitleCONTRIBUTIONS OF LEFT-HANDED HELICAL RESIDUES TO THE STRUCTURE AND STABILITY OF 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 / Lysozyme domain superfamily / Phage lysozyme / Lysozyme / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / Resolution: 1.85 Å
AuthorsNicholson, H. / Matthews, B.W.
Citation
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.
#1: Journal: To be Published
Title: Structural Studies of Mutants of T4 Lysozyme that Alter Hydrophobic Stabilization
Authors: Matsumura, M. / Wozniak, J.A. / Dao-Pin, S. / Matthews, B.W.
#2: 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.
#3: 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.
#4: 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.
#5: 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.
#6: 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.
#7: 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.
#8: 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.
#9: 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.
#10: 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.
#11: 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.
#12: 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.
#13: 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.
#14: 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.
#15: 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.
#16: Journal: Biochem.Biophys.Res.Commun. / Year: 1977
Title: Atomic Coordinates for T4 Phage Lysozyme
Authors: Remington, S.J. / Teneyck, L.F. / Matthews, B.W.
#17: Journal: Biochim.Biophys.Acta / Year: 1975
Title: Comparison of the Predicted and Observed Secondary Structure of T4 Phage Lysozyme
Authors: Matthews, B.W.
#18: 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.
#19: Journal: J.Mol.Biol. / Year: 1973
Title: Crystallographic Data for Lysozyme from Bacteriophage T4
Authors: Matthews, B.W. / Dahlquist, F.W. / Maynard, A.Y.
History
DepositionMay 1, 1989Processing site: BNL
Revision 1.0Jan 15, 1990Provider: 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 / 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 / pdbx_validate_torsion / struct_ref_seq_dif
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 / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _struct_ref_seq_dif.details
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 IN REFERENCE 15 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


Theoretical massNumber of molelcules
Total (without water)18,6051
Polymers18,6051
Non-polymers00
Water2,774154
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.100, 61.100, 97.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Atom site foot note1: SEE REMARK 6.
Components on special symmetry positions
IDModelComponents
11A-552-

HOH

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Components

#1: Protein T4 LYSOZYME


Mass: 18605.416 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 2.81 Å3/Da / Density % sol: 56.21 %
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
Highest resolution: 1.85 Å / Num. obs: 12130 / Rmerge(I) obs: 0.093

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Processing

SoftwareName: TNT / Classification: refinement
RefinementResolution: 1.85→6 Å / Rfactor obs: 0.173
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: 1.85→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1305 0 0 154 1459
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.017
X-RAY DIFFRACTIONt_angle_deg2.47
X-RAY DIFFRACTIONt_dihedral_angle_d21.25
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.014
X-RAY DIFFRACTIONt_gen_planes21.25
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.173
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_d
X-RAY DIFFRACTIONt_angle_deg2.5

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