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- PDB-2lzm: STRUCTURE OF BACTERIOPHAGE T4 LYSOZYME REFINED AT 1.7 ANGSTROMS R... -

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Entry
Database: PDB / ID: 2lzm
TitleSTRUCTURE OF BACTERIOPHAGE T4 LYSOZYME REFINED AT 1.7 ANGSTROMS RESOLUTION
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
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / Resolution: 1.7 Å
AuthorsWeaver, L.H. / Matthews, B.W.
Citation
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.
#1: 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.
#2: 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.
#3: 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.
#4: 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.
#5: 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.
#6: Journal: Biochem.Biophys.Res.Commun. / Year: 1977
Title: Atomic Coordinates for T4 Phage Lysozyme
Authors: Remington, S.J. / Teneyck, L.F. / Matthews, B.W.
#7: Journal: Biochim.Biophys.Acta / Year: 1975
Title: Comparison of the Predicted and Observed Secondary Structure of T4 Phage Lysozyme
Authors: Matthews, B.W.
#8: 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.
#9: Journal: J.Mol.Biol. / Year: 1973
Title: Crystallographic Data for Lysozyme from Bacteriophage T4
Authors: Matthews, B.W. / Dahlquist, F.W. / Maynard, A.Y.
#10: Journal: Atlas of Protein Sequence and Structure (Data Section)
Year: 1972
History
DepositionAug 18, 1986Processing site: BNL
SupersessionOct 24, 1986ID: 1LZM
Revision 1.0Oct 24, 1986Provider: 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 1.4Jul 22, 2020Group: Data collection / Other / Refinement description
Category: diffrn / diffrn_detector ...diffrn / diffrn_detector / diffrn_radiation / diffrn_radiation_wavelength / diffrn_source / pdbx_database_status / software
Item: _diffrn.ambient_pressure / _diffrn.ambient_temp / _pdbx_database_status.status_code_sf
Revision 1.5Jun 30, 2021Group: Data collection / Category: diffrn_detector / diffrn_source / Item: _diffrn_detector.detector / _diffrn_source.source
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 / database_2 / database_PDB_matrix / entity_src_gen / pdbx_database_remark / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion
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_rmsd_bond.bond_deviation / _pdbx_validate_rmsd_bond.bond_value / _pdbx_validate_torsion.psi
Details: ORTHOGONAL X,Y,Z AXES WERE REALIGNED FROM A*,B,C TO A,B*,C CRYSTALLOGRAPHIC DIRECTIONS
Provider: repository / Type: Remediation
Revision 2.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
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 5 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)18,6621
Polymers18,6621
Non-polymers00
Water2,126118
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

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Components

#1: Protein T4 LYSOZYME


Mass: 18662.467 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 / References: UniProt: P00720, lysozyme
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 56.13 %
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 phospahte11
62.2 M11NaH2PO4
71.8 M11K2HPO4

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Data collection

DiffractionAmbient pressure: 101 kPa / Mean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-21 / Target: Cu / Voltage: 40 kV
DetectorType: OSCILLATION CAMERA / Detector: FILM / Details: Kodak No-Screen X-ray film
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray / Wavelength: 1.5418 Å
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.7 Å / Num. obs: 32603 / Num. measured all: 70201

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Processing

Software
NameClassification
TNTrefinement
AGROVATA / ROTAVATAdata scaling
RefinementRfactor obs: 0.193 / Highest resolution: 1.7 Å
Refinement stepCycle: LAST / Highest resolution: 1.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1309 0 0 118 1427
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.019
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
Lowest resolution: 6 Å / Highest resolution: 1.7 Å / Rfactor obs: 0.193
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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