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- PDB-198l: THERMODYNAMIC AND STRUCTURAL COMPENSATION IN "SIZE-SWITCH" CORE-R... -

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Basic information

Entry
Database: PDB / ID: 198l
TitleTHERMODYNAMIC AND STRUCTURAL COMPENSATION IN "SIZE-SWITCH" CORE-REPACKING VARIANTS OF T4 LYSOZYME
ComponentsLYSOZYME
KeywordsHYDROLASE (O-GLYCOSYL) / CAVITIES / CORE-PACKING / PROTEIN STABILITY
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
BETA-MERCAPTOETHANOL / Endolysin
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsBaldwin, E. / Xu, J. / Hajiseyedjavadi, O. / Matthews, B.W.
Citation
Journal: J.Mol.Biol. / Year: 1996
Title: Thermodynamic and structural compensation in "size-switch" core repacking variants of bacteriophage T4 lysozyme.
Authors: Baldwin, E. / Xu, J. / Hajiseyedjavadi, O. / Baase, W.A. / Matthews, B.W.
#1: Journal: Science / Year: 1993
Title: The Role of Backbone Flexibility in the Accommodation of Variants that Repack the Core of T4 Lysozyme
Authors: Baldwin, E.P. / Hajiseyedjavadi, O. / Baase, W.A. / Matthews, B.W.
#2: Journal: Science / Year: 1989
Title: Control of Enzyme Activity by an Engineered Disulfide Bond
Authors: Matsumura, M. / Matthews, B.W.
#3: Journal: Methods Enzymol. / Year: 1989
Title: Expression and Nitrogen-15 Labeling of Proteins for Proton and Nitrogen-15 Nuclear Magnetic Resonance
Authors: Muchmore, D.C. / Mcintosh, L.P. / Russell, C.B. / Anderson, D.E. / Dahlquist, F.W.
#4: 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
DepositionNov 6, 1995Processing site: BNL
Revision 1.0Mar 8, 1996Provider: 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 1.4Jul 22, 2020Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: diffrn / diffrn_detector ...diffrn / diffrn_detector / diffrn_radiation / diffrn_source / pdbx_database_status / software / struct_ref_seq_dif
Item: _diffrn.ambient_pressure / _diffrn_detector.details ..._diffrn.ambient_pressure / _diffrn_detector.details / _diffrn_detector.type / _diffrn_radiation.monochromator / _diffrn_radiation.pdbx_diffrn_protocol / _diffrn_radiation.pdbx_wavelength_list / _diffrn_source.source / _diffrn_source.target / _diffrn_source.type / _pdbx_database_status.status_code_sf / _struct_ref_seq_dif.details
Revision 1.5Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)18,8565
Polymers18,6281
Non-polymers2274
Water2,558142
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.100, 61.100, 96.100
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


Mass: 18628.363 Da / Num. of mol.: 1 / Mutation: C54T, C97A, L121A, A129L
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
Description: MUTANT GENE WAS DERIVED FROM SITE-DIRECTED MUTAGENESIS OF THE GENE FOR CYS-FREE WILDTYPE T4 LYSOZYME IN M13 USING THE METHOD OF KUNKEL AND THE VECTOR SYSTEM DESCRIBED IN REFERENCE 3 BELOW
Variant: CYS-FREE WILDTYPE T4 / Plasmid: M13 / Production host: Escherichia coli (E. coli) / References: UniProt: P00720, lysozyme
#2: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 2.78 Å3/Da / Density % sol: 55.74 %
Crystal growpH: 6.7 / Details: pH 6.7
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
120 mg/mlprotein11
20.55 M11NaCl
314 mMmercaptoethanol11
41 mM11MgCl2
50.01 Msodium phospahte11m
62.2 M11NaH2PO4
71.8 M11K2HPO4

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Data collection

DiffractionAmbient pressure: 101 kPa / Mean temperature: 298 K
Diffraction sourceSource: rotating-anode X-ray tube / Type: RIGAKU RU200 / Wavelength: 1.5418 / Target: Cu
DetectorType: AREA DETECTOR / Detector: AREA DETECTOR / Details: Xuong-Hamlin
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
ReflectionRmerge(I) obs: 0.041
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 10 Å / Num. obs: 12672 / % possible obs: 84 % / Rmerge(I) obs: 0.041

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Processing

Software
NameVersionClassification
TNTrefinement
XUONG-HAMLIN(DETECTOR SYSTEM)data reduction
Xengen (HOWARD, NIELSEN, XUONG)data scaling
RefinementResolution: 2→10 Å / σ(F): 0
Details: MUTANT SPACE GROUP, P 32 2 1, IS ISOMORPHOUS TO WILD TYPE. STARTING COORDINATES WERE BASED ON THE CYS-FREE WILD-TYPE MODEL.
RfactorNum. reflection% reflection
obs0.158 12672 84 %
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1292 0 10 143 1445
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.014
X-RAY DIFFRACTIONt_angle_deg2
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
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.013
X-RAY DIFFRACTIONt_angle_deg1.9

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