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- PDB-1lw9: Multiple methionine substitutions are tolerated in T4 lysozyme an... -

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Basic information

Entry
Database: PDB / ID: 1lw9
TitleMultiple methionine substitutions are tolerated in T4 lysozyme and have coupled effects on folding and stability
ComponentsLYSOZYME
KeywordsHYDROLASE / hydrolase (o-glycosyl) / T4 lysozyme / methionine core mutant / protein engineering / protein folding
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
2-HYDROXYETHYL DISULFIDE / : / Endolysin
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsGassner, N.C. / Baase, W.A. / Mooers, B.H.M. / Busam, R.D. / Weaver, L.H. / Lindstrom, J.D. / Quillin, M.L. / Matthews, B.W.
CitationJournal: Biophys.Chem. / Year: 2003
Title: Multiple methionine substitutions are tolerated in T4 lysozyme and have coupled effects on folding and stability.
Authors: Gassner, N.C. / Baase, W.A. / Mooers, B.H. / Busam, R.D. / Weaver, L.H. / Lindstrom, J.D. / Quillin, M.L. / Matthews, B.W.
History
DepositionMay 30, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 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)18,8935
Polymers18,6281
Non-polymers2644
Water3,567198
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.207, 60.207, 95.375
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: 18628.363 Da / Num. of mol.: 1 / Mutation: 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 / Plasmid: phs1403 / Production host: Escherichia coli (E. coli) / Strain (production host): RR1 / References: UniProt: P00720, lysozyme
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-HED / 2-HYDROXYETHYL DISULFIDE


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / 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: 2.68 Å3/Da / Density % sol: 53.8 %
Description: 1) Working and test sets were not combined during the last cycles of refinement. 2) OVERALL B-VALUES: B11=B12=B22=2.5 B33=-4.99 B13=B23=0.00
Crystal growpH: 6.7 / Details: pH 6.7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 14, 2002 / Details: MIRRORS
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.45→27.1 Å / Num. obs: 35919 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 21.8 Å2 / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 4.8
Reflection shellResolution: 1.45→1.53 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.316 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.316 / % possible all: 99

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
TNTrefinement
CCP4(SCALA)data scaling
TNTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1L63

1l63


Resolution: 1.45→23 Å / Isotropic thermal model: TNT BCORRELATION LIBRARY / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: TNT'S TNTGEO_V010.DAT
Details: THE USE OF RFREE FOR THIS STRUCTURE during refinement was not very valid since the starting model had been refined against 1.75 Angstrom room temperature data (~15000 reflections). ...Details: THE USE OF RFREE FOR THIS STRUCTURE during refinement was not very valid since the starting model had been refined against 1.75 Angstrom room temperature data (~15000 reflections). Nonetheless, for the benefit of future workers, this structure (1LW9) was NOT refined against both the test and working sets during the final stage of refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.254 1776 5 %RANDOM
Rwork0.197 ---
all0.2 35772 --
obs0.2 33992 94 %-
Solvent computationSolvent model: TNT'S MODEL / Bsol: 232.25 Å2 / ksol: 0.86 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.5 Å22.5 Å20 Å2
2--2.5 Å20 Å2
3----4.99 Å2
Refinement stepCycle: LAST / Resolution: 1.45→23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1323 0 11 206 1540
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.017
X-RAY DIFFRACTIONt_angle_deg2.641
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd

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