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- PDB-148l: A COVALENT ENZYME-SUBSTRATE INTERMEDIATE WITH SACCHARIDE DISTORTI... -

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Entry
Database: PDB / ID: 148l
TitleA COVALENT ENZYME-SUBSTRATE INTERMEDIATE WITH SACCHARIDE DISTORTION IN A MUTANT T4 LYSOZYME
Components
  • SUBSTRATE CLEAVED FROM CELL WALL OF ESCHERICHIA COLI
  • T4 LYSOZYME
KeywordsHYDROLASE/HYDROLASE SUBSTRATE / O-GLYCOSYL / HYDROLASE-HYDROLASE SUBSTRATE complex
Function / homologyT4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme-like domain superfamily / Endolysin T4 type / Phage lysozyme / cytolysis by virus of host cell / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity ...T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme-like domain superfamily / Endolysin T4 type / Phage lysozyme / cytolysis by virus of host cell / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / cytolysis / host cell cytoplasm / defense response to bacterium / Endolysin
Function and homology information
Specimen sourceEnterobacteria phage T4 (bacteriophage)
ESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / 1.9 Å resolution
AuthorsKuroki, R. / Weaver, L.H. / Matthews, B.W.
Citation
Journal: Science / Year: 1993
Title: A covalent enzyme-substrate intermediate with saccharide distortion in a mutant T4 lysozyme.
Authors: Kuroki, R. / Weaver, L.H. / 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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Oct 27, 1993 / Release: Apr 30, 1994
RevisionDateData content typeGroupCategoryItemProviderType
1.0Apr 30, 1994Structure modelrepositoryInitial release
1.1May 22, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance
1.3Jul 27, 2011Structure modelAtomic model / Database references / Derived calculations / Non-polymer description / Structure summary
1.4Nov 29, 2017Structure modelDerived calculations / Otherpdbx_database_status / struct_conf / struct_conf_type_pdbx_database_status.process_site
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 J.MOL.BIOL., V. 118, P. 81, 1978 BE CONSULTED FOR THESE SUBTLETIES.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
E: T4 LYSOZYME
S: SUBSTRATE CLEAVED FROM CELL WALL OF ESCHERICHIA COLI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7105
Polyers19,1182
Non-polymers5933
Water2,522140
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)50.900, 67.300, 49.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP 21 21 2
Atom site foot note1: RESIDUES 162 - 164 IN WILD-TYPE AND ALL MUTANT LYSOZYMES ARE EXTREMELY MOBILE. THUS THE COORDINATES FOR THESE RESIDUES ARE VERY UNRELIABLE. THIS ENTRY DOES NOT INCLUDE RESIDUES 163 AND 164.

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Components

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Protein/peptide , 2 types, 2 molecules ES

#1: Protein/peptide T4 LYSOZYME


Mass: 18656.373 Da / Num. of mol.: 1
Source: (gene. exp.) Enterobacteria phage T4 (bacteriophage)
Genus: T4-like viruses / Species: Enterobacteria phage T4 sensu lato / Plasmid name: M13 / References: UniProt: P00720, lysozyme
#2: Protein/peptide SUBSTRATE CLEAVED FROM CELL WALL OF ESCHERICHIA COLI


Mass: 461.466 Da / Num. of mol.: 1 / Source: (natural) ESCHERICHIA COLI (E. coli) / Tissue: CELL WALL

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Non-polymers , 4 types, 143 molecules

#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Formula: C2H6OS / 2-Mercaptoethanol
#4: Chemical ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 1 / Formula: C8H15NO6 / N-Acetylglucosamine
#5: Chemical ChemComp-MUB / N-ACETYLMURAMIC ACID


Mass: 293.270 Da / Num. of mol.: 1 / Formula: C11H19NO8 / N-Acetylmuramic acid
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / Formula: H2O / Water

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.17 / Density percent sol: 43.25 %

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
D resolution high: 1.9 Å / Number obs: 11889 / Percent possible obs: 85

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Processing

SoftwareName: TNT / Classification: refinement
RefineDetails: RESIDUES 162 - 164 IN WILD-TYPE AND ALL MUTANT LYSOZYMES ARE EXTREMELY MOBILE. THUS THE COORDINATES FOR THESE RESIDUES ARE VERY UNRELIABLE. THIS ENTRY DOES NOT INCLUDE RESIDUES 163 AND 164. MUTANT SPACE GROUP, P 21 21 2, IS NONISOMORPHOUS TO WILD TYPE. STARTING COORDINATES WERE BASED ON THE WILD-TYPE MODEL.
Sigma F: 0
Least-squares processR factor obs: 0.168 / Highest resolution: 1.9 Å / Lowest resolution: 2 Å / Number reflection obs: 11889
Refine hist #LASTHighest resolution: 1.9 Å / Lowest resolution: 2 Å
Number of atoms included #LASTProtein: 1327 / Nucleic acid: 0 / Ligand: 36 / Solvent: 140 / Total: 1503
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.014
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
Software
*PLUS
Name: TNT / Classification: refinement
Least-squares process
*PLUS
R factor obs: 0.168
Refine LS restraints
*PLUS
Refine IDType
X-RAY DIFFRACTIONt_angle_d
X-RAY DIFFRACTIONt_angle_deg

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