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- PDB-1lwg: Multiple Methionine Substitutions are Tolerated in T4 Lysozyme an... -

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Basic information

Entry
Database: PDB / ID: 1lwg
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 / : / PHOSPHATE ION / Endolysin
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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.M.
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 31, 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: Derived calculations / Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 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_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_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 1.5Feb 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)19,5049
Polymers18,8011
Non-polymers7038
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: Lysozyme
hetero molecules

A: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,00818
Polymers37,6012
Non-polymers1,40616
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area4070 Å2
ΔGint-70 kcal/mol
Surface area15890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.425, 60.425, 90.388
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Lysozyme / Lysis protein / Muramidase / Endolysin


Mass: 18800.719 Da / Num. of mol.: 1
Mutation: C54T,L84M,V87M,L91M,C97A,L99M,V111M,L118M,L121M,L133M
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

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Non-polymers , 5 types, 152 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-HED / 2-HYDROXYETHYL DISULFIDE


Mass: 154.251 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O2S2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 2.53 Å3/Da / Density % sol: 51.45 %
Crystal growMethod: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.77487 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 10, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.77487 Å / Relative weight: 1
ReflectionResolution: 1.7→19.8 Å / Num. all: 21411 / Num. obs: 21345 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 21.4 Å2 / Rmerge(I) obs: 0.052 / Rsym value: 0.052 / Net I/σ(I): 7.1
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.284 / Mean I/σ(I) obs: 2.7 / Num. unique all: 2976 / Rsym value: 0.284 / % possible all: 96.8

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Processing

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

1l63


Resolution: 1.7→19.8 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Residues ASN 163 and LEU 164 are missing in the electron density.
RfactorNum. reflection
Rwork0.194 -
all0.194 21345
obs0.194 21345
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.67 Å21.67 Å20 Å2
2--1.67 Å20 Å2
3----3.33 Å2
Refinement stepCycle: LAST / Resolution: 1.7→19.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1294 0 33 144 1471
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg2.844
X-RAY DIFFRACTIONt_bond_d0.019
X-RAY DIFFRACTIONt_dihedral_angle_d16.103

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