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- PDB-1kni: Stabilizing Disulfide Bridge Mutant of T4 Lysozyme -

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Basic information

Entry
Database: PDB / ID: 1kni
TitleStabilizing Disulfide Bridge Mutant of T4 Lysozyme
ComponentsLYSOZYME
KeywordsHYDROLASE / Glycosidase / Bacteriolytic enzyme
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
BETA-MERCAPTOETHANOL / Endolysin
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / Rigid body / Resolution: 1.7 Å
AuthorsJacobson, R.H. / Matsumura, M. / Faber, H.R. / Matthews, B.W.
CitationJournal: Protein Sci. / Year: 1992
Title: Structure of a stabilizing disulfide bridge mutant that closes the active-site cleft of T4 lysozyme.
Authors: Jacobson, R.H. / Matsumura, M. / Faber, H.R. / Matthews, B.W.
History
DepositionDec 18, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Jul 22, 2020Group: Advisory / Data collection ...Advisory / Data collection / Other / Refinement description
Category: cell / diffrn ...cell / diffrn / diffrn_detector / diffrn_radiation / diffrn_source / pdbx_database_status / pdbx_validate_symm_contact / software
Item: _cell.length_a / _cell.length_b ..._cell.length_a / _cell.length_b / _cell.length_c / _diffrn.ambient_pressure / _diffrn.ambient_temp / _diffrn_detector.details / _diffrn_detector.detector / _diffrn_detector.type / _diffrn_radiation.monochromator / _diffrn_radiation.pdbx_wavelength_list / _diffrn_source.source / _diffrn_source.target / _diffrn_source.type / _diffrn_source.voltage / _pdbx_database_status.status_code_sf / _pdbx_validate_symm_contact.dist / _software.name
Revision 1.5Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LYSOZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7463
Polymers18,6321
Non-polymers1142
Water1,982110
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.300, 62.300, 95.200
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 LYSOZYME / / LYSIS PROTEIN / MURAMIDASE / ENDOLYSIN


Mass: 18632.441 Da / Num. of mol.: 1 / Mutation: T21C,T142C,C54T,C97A
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 / Production host: Escherichia coli (E. coli) / References: UniProt: P00720, lysozyme
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.86 Å3/Da / Density % sol: 56.93 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
121.5 mg/mlprotein1drop
20.1 Msodium potassium phosphate1droppH6.6
30.55 M1dropNaCl
40.02 %1dropNaN3
51.9 MNa/KPO41reservoirpH7.1
60.24 M1reservoirNaCl
730-140 mMbeta-mercaptoethanol1reservoir

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Data collection

DiffractionAmbient pressure: 101 kPa / Mean temperature: 298 K
Diffraction sourceSource: rotating-anode X-ray tube / Type: ELLIOTT GX-21 / Wavelength: 1.5418 Å / Target: Cu / Voltage: 40 kV
DetectorType: OSCILLATION CAMERA / Detector: photographic film / Date: Jul 1, 1991 / 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 wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 1.7 Å / Num. obs: 15778 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.071

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Processing

Software
NameVersionClassification
ROTAVATAdata reduction
TNTrefinement
AGROVATA / ROTAVATA(AGROVATAdata scaling
AGROVATA / ROTAVATAdata scaling
TNTphasing
RefinementMethod to determine structure: Rigid body
Starting model: WT* T4 lysozyme

Highest resolution: 1.7 Å / Isotropic thermal model: Isotropic / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: residues 163 and 164 are missing in the electron density.
RfactorNum. reflection
all0.176 -
obs-15778
Refinement stepCycle: LAST / Highest resolution: 1.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1290 0 5 110 1405
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.019
X-RAY DIFFRACTIONt_angle_deg2.9
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.7 Å / σ(F): 0 / Rfactor all: 0.176
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: t_angle_deg / Dev ideal: 2.9

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