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- PDB-150l: CONSERVATION OF SOLVENT-BINDING SITES IN 10 CRYSTAL FORMS OF T4 L... -

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Basic information

Entry
Database: PDB / ID: 150l
TitleCONSERVATION OF SOLVENT-BINDING SITES IN 10 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: 2.2 Å
AuthorsFaber, H.R. / Matthews, B.W.
Citation
Journal: Protein Sci. / Year: 1994
Title: Conservation of solvent-binding sites in 10 crystal forms of T4 lysozyme.
Authors: Zhang, X.J. / Matthews, B.W.
#1: Journal: Nature / Year: 1990
Title: A Mutant T4 Lysozyme Displays Five Different Crystal Conformations
Authors: Faber, H.R. / Matthews, B.W.
History
DepositionJan 25, 1994Processing site: BNL
Revision 1.0Apr 30, 1994Provider: 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


Theoretical massNumber of molelcules
Total (without water)74,5784
Polymers74,5784
Non-polymers00
Water2,954164
1
A: T4 LYSOZYME


Theoretical massNumber of molelcules
Total (without water)18,6441
Polymers18,6441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: T4 LYSOZYME


Theoretical massNumber of molelcules
Total (without water)18,6441
Polymers18,6441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: T4 LYSOZYME


Theoretical massNumber of molelcules
Total (without water)18,6441
Polymers18,6441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: T4 LYSOZYME


Theoretical massNumber of molelcules
Total (without water)18,6441
Polymers18,6441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.200, 73.800, 150.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
T4 LYSOZYME


Mass: 18644.430 Da / Num. of mol.: 4
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


Mass: 18.015 Da / Num. of mol.: 164 / 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: 2.69 Å3/Da / Density % sol: 54.24 %
Crystal grow
*PLUS
Method: unknown / PH range low: 7.1 / PH range high: 6.7
Components of the solutions
*PLUS
Conc.: 2.0 M / Common name: phosphate

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

SoftwareName: TNT / Classification: refinement
RefinementResolution: 2.2→6 Å / σ(F): 0 /
RfactorNum. reflection
obs0.21 32548
Refinement stepCycle: LAST / Resolution: 2.2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5163 0 0 164 5327
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.021
X-RAY DIFFRACTIONt_angle_deg2.69
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
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: t_angle_d / Dev ideal: 2.69

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