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- PDB-169l: PROTEIN FLEXIBILITY AND ADAPTABILITY SEEN IN 25 CRYSTAL FORMS OF ... -

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Basic information

Entry
Database: PDB / ID: 169l
TitlePROTEIN FLEXIBILITY AND ADAPTABILITY SEEN IN 25 CRYSTAL FORMS OF 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
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / Resolution: 3 Å
AuthorsZhang, X.-J. / Matthews, B.W.
Citation
Journal: J.Mol.Biol. / Year: 1995
Title: Protein flexibility and adaptability seen in 25 crystal forms of T4 lysozyme.
Authors: Zhang, X.J. / Wozniak, J.A. / Matthews, B.W.
#1: 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.
History
DepositionMar 24, 1995Processing site: BNL
Revision 1.0Jul 10, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: 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 1.4Feb 7, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: T4 LYSOZYME
B: T4 LYSOZYME
C: T4 LYSOZYME
D: T4 LYSOZYME
E: T4 LYSOZYME


Theoretical massNumber of molelcules
Total (without water)90,9055
Polymers90,9055
Non-polymers00
Water00
1
A: T4 LYSOZYME


Theoretical massNumber of molelcules
Total (without water)18,1811
Polymers18,1811
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: T4 LYSOZYME


Theoretical massNumber of molelcules
Total (without water)18,1811
Polymers18,1811
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: T4 LYSOZYME


Theoretical massNumber of molelcules
Total (without water)18,1811
Polymers18,1811
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: T4 LYSOZYME


Theoretical massNumber of molelcules
Total (without water)18,1811
Polymers18,1811
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: T4 LYSOZYME


Theoretical massNumber of molelcules
Total (without water)18,1811
Polymers18,1811
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.400, 112.300, 135.200
Angle α, β, γ (deg.)90.00, 91.70, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
T4 LYSOZYME


Mass: 18180.969 Da / Num. of mol.: 5
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

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.37 Å3/Da / Density % sol: 63.52 %
Crystal
*PLUS
Density % sol: 64 %
Crystal grow
*PLUS
pH: 6.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
117 %(w/v)PEG34001reservoir
20.2 Mphosphate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

SoftwareName: TNT / Classification: refinement
RefinementResolution: 3→6 Å /
RfactorNum. reflection
obs0.161 12424
Refinement stepCycle: LAST / Resolution: 3→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6290 0 0 0 6290
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.015
X-RAY DIFFRACTIONt_angle_deg2.4
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

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