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- PDB-2o7a: T4 lysozyme C-terminal fragment -

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Basic information

Entry
Database: PDB / ID: 2o7a
TitleT4 lysozyme C-terminal fragment
ComponentsLysozyme
KeywordsHYDROLASE / Protein folding / protein stability / lysozyme / circular permutant
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
ACETATE ION / Endolysin
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.84 Å
AuthorsEchols, N. / Kwon, E. / Marqusee, S.M. / Alber, T.
CitationJournal: Protein Sci. / Year: 2007
Title: Exploring subdomain cooperativity in T4 lysozyme I: Structural and energetic studies of a circular permutant and protein fragment.
Authors: Cellitti, J. / Llinas, M. / Echols, N. / Shank, E.A. / Gillespie, B. / Kwon, E. / Crowder, S.M. / Dahlquist, F.W. / Alber, T. / Marqusee, S.
History
DepositionDec 10, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.5Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn / Item: _software.name / _struct_conn.pdbx_leaving_atom_flag
Revision 1.6Oct 20, 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 1.7Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 999SEQUENCE Residues 171-182 correspond to residues 1-12 in the wild-type structure. The initial 12 ...SEQUENCE Residues 171-182 correspond to residues 1-12 in the wild-type structure. The initial 12 residues have been moved to the C-terminus, with a 6-residue linker (SGGGGA) in between.

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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)14,1333
Polymers14,0381
Non-polymers942
Water5,945330
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.634, 50.017, 32.711
Angle α, β, γ (deg.)90.00, 90.86, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 14038.006 Da / Num. of mol.: 1 / Mutation: 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 / Gene: E / Plasmid: pET27K / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta/pLacI / References: UniProt: P00720, lysozyme
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 330 / 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: 1.84 Å3/Da / Density % sol: 33.26 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 100 mM NaCacodylate pH 5.0, 200 mM NaAcetate, 26% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.82653 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 30, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.82653 Å / Relative weight: 1
ReflectionResolution: 0.84→20 Å / Num. all: 92458 / Num. obs: 92458 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 4.64 Å2 / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Net I/σ(I): 31.8
Reflection shellResolution: 0.84→0.87 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.224 / Mean I/σ(I) obs: 2.5 / Num. unique all: 9108 / Rsym value: 0.224 / % possible all: 99

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Processing

Software
NameClassification
SHELXL-97refinement
MOLREPphasing
ELVESrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1sx7
Resolution: 0.84→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1078 4630 -RANDOM
Rwork0.0904 ---
obs0.0904 92310 99.7 %-
all-92310 --
Refinement stepCycle: LAST / Resolution: 0.84→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1197 0 5 364 1566
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.015
X-RAY DIFFRACTIONs_angle_d0.037
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.049

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