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- PDB-2igc: Structure of Spin labeled T4 Lysozyme Mutant T115R1A -

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Basic information

Entry
Database: PDB / ID: 2igc
TitleStructure of Spin labeled T4 Lysozyme Mutant T115R1A
ComponentsLysozyme
KeywordsHYDROLASE / Nitroxide / Spin Label / EPR / T4 Lysozyme
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
Chem-MTN / Endolysin
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsGuo, Z. / Cascio, D. / Hideg, K. / Hubbell, W.L.
CitationJournal: Protein Sci. / Year: 2007
Title: Structural determinants of nitroxide motion in spin-labeled proteins: Tertiary contact and solvent-inaccessible sites in helix G of T4 lysozyme.
Authors: Guo, Z. / Cascio, D. / Hideg, K. / Kalai, T. / Hubbell, W.L.
History
DepositionSep 22, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 27, 2011Group: Non-polymer description
Revision 1.4Oct 20, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.6Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)18,8952
Polymers18,6301
Non-polymers2641
Water4,035224
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.777, 59.777, 95.373
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: 18630.402 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 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P00720, lysozyme
#2: Chemical ChemComp-MTN / S-[(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl] methanesulfonothioate / MTSL


Mass: 264.385 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H18NO3S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.61 Å3/Da / Density % sol: 53.71 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: 1.8 M NaH2PO4, 1.8 M K2HPO4, 240 mM NaCl, 40 mM 2-hydroxyethyl disulfide, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 11, 2002 / Details: Parabolic collimating mirrors
RadiationMonochromator: Sagitally Focused Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.4→100 Å / Num. all: 38868 / Num. obs: 38868 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.12 % / Biso Wilson estimate: 13.9 Å2 / Rsym value: 0.067 / Χ2: 1.019 / Net I/σ(I): 30.1
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.291 / Mean I/σ(I) obs: 4.46 / Num. unique all: 3594 / Rsym value: 0.291 / Χ2: 0.758 / % possible all: 92.7

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
EPMRphasing
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LZM

3lzm


Resolution: 1.4→10 Å / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1975 1945 -Random
Rwork0.154 ---
obs0.1527 36805 93.5 %-
all-36805 --
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1544
Refinement stepCycle: LAST / Resolution: 1.4→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1308 0 12 224 1544
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.012
X-RAY DIFFRACTIONs_angle_d0.028
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0237
X-RAY DIFFRACTIONs_zero_chiral_vol0.053
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.065
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.017
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.004
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.037
X-RAY DIFFRACTIONs_approx_iso_adps0.084

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