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- PDB-137l: STRUCTURAL BASIS OF AMINO ACID ALPHA HELIX PROPENSITY -

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Basic information

Entry
Database: PDB / ID: 137l
TitleSTRUCTURAL BASIS OF AMINO ACID ALPHA HELIX PROPENSITY
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
AuthorsBlaber, M. / Matthews, B.W.
Citation
Journal: Science / Year: 1993
Title: Structural basis of amino acid alpha helix propensity.
Authors: Blaber, M. / Zhang, X.J. / Matthews, B.W.
#1: Journal: Science / Year: 1989
Title: Control of Enzyme Activity by an Engineered Disulfide Bond
Authors: Matsumura, M. / Matthews, B.W.
#2: 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
DepositionAug 17, 1993Processing site: BNL
Revision 1.0Jul 31, 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 1.4Jan 15, 2020Group: Advisory / Database references / Derived calculations
Category: pdbx_distant_solvent_atoms / pdbx_struct_assembly ...pdbx_distant_solvent_atoms / pdbx_struct_assembly / pdbx_struct_assembly_gen / struct_ref_seq_dif
Item: _struct_ref_seq_dif.details
Revision 1.5Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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


Theoretical massNumber of molelcules
Total (without water)37,3772
Polymers37,3772
Non-polymers00
Water4,414245
1
A: T4 LYSOZYME


Theoretical massNumber of molelcules
Total (without water)18,6881
Polymers18,6881
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: T4 LYSOZYME


Theoretical massNumber of molelcules
Total (without water)18,6881
Polymers18,6881
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.070, 55.910, 59.860
Angle α, β, γ (deg.)90.00, 103.56, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein T4 LYSOZYME


Mass: 18688.459 Da / Num. of mol.: 2
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.: 245 / 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: 2.35 Å3/Da / Density % sol: 47.72 %
Crystal grow
*PLUS
Method: unknown / pH: 6.7
Details: S. Dao-pin, (1990) Proteins Struct. Funct. Gen., 7, 198.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11.05 M11K2HPO4
21.26 M11NaH2PO4
30.23 M11NaCl
41.4 mMbeta-mercaptoethanol11

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

SoftwareName: TNT / Classification: refinement
RefinementResolution: 1.85→6 Å / σ(F): 2
Details: MUTANT SPACE GROUP, P2(1), IS NON-ISOMORPHOUS TO WILD TYPE P3(2)21. THERE ARE TWO MOLECULES IN THE ASYMMETRIC UNIT, AND THE POSITION OF EACH OF THESE WAS SOLVED BY A SIX-DIMENSIONAL SEARCH ...Details: MUTANT SPACE GROUP, P2(1), IS NON-ISOMORPHOUS TO WILD TYPE P3(2)21. THERE ARE TWO MOLECULES IN THE ASYMMETRIC UNIT, AND THE POSITION OF EACH OF THESE WAS SOLVED BY A SIX-DIMENSIONAL SEARCH USING THE WILD TYPE COORDINATES. RESIDUES 162 - 164 IN WILD-TYPE AND ALL MUTANT LYSOZYMES ARE EXTREMELY MOBILE. THUS THE COORDINATES FOR THESE RESIDUES ARE VERY UNRELIABLE. IN THIS ENTRY CHAIN A DOES NOT INCLUDE RESIDUES 163 AND 164 AND CHAIN B DOES INCLUDE THEM.
RfactorNum. reflection
obs0.15 20448
Refinement stepCycle: LAST / Resolution: 1.85→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2611 0 0 245 2856
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.012
X-RAY DIFFRACTIONt_angle_deg1.9
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: 0.15
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: t_angle_d / Dev ideal: 1.9

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