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- PDB-2o4w: T4 lysozyme circular permutant -

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Basic information

Entry
Database: PDB / ID: 2o4w
TitleT4 lysozyme circular permutant
ComponentsLysozyme
KeywordsHYDROLASE / Protein folding / protein stability / protein engineering / 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 / Lysozyme domain superfamily / Phage lysozyme / Lysozyme / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLlinas, M. / Crowder, S.M. / Echols, N. / Alber, T. / Marqusee, S.
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 5, 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: Source and taxonomy / Category: entity_src_gen
Revision 1.4Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.5Oct 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 1.6Aug 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)19,2183
Polymers19,1471
Non-polymers712
Water3,063170
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.118, 60.118, 96.531
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-516-

HOH

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Components

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


Mass: 19146.906 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 / Gene: E / Plasmid: pET27K / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta/pLacI / References: UniProt: P00720, lysozyme
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 2.63 Å3/Da / Density % sol: 53.22 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: 0.9 M K2HPO4, 1.1 M NaH2PO4, pH 6.9, 0.25 M NaCl, 49.0 mM oxidized B-mercaptoethanol, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jun 1, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→35.4 Å / Num. all: 16286 / Num. obs: 16286 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 18.3 Å2 / Rmerge(I) obs: 0.098 / Rsym value: 0.098 / Net I/σ(I): 10.4
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.396 / Mean I/σ(I) obs: 2.8 / Num. unique all: 2354 / Rsym value: 0.396 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
ELVESrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1sx7

1sx7


Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.917 / SU B: 2.569 / SU ML: 0.079 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.131 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21288 821 5.1 %RANDOM
Rwork0.17454 ---
all0.17646 16256 --
obs0.17646 15435 98.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.359 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.01 Å20 Å2
2--0.02 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1277 0 2 170 1449
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221297
X-RAY DIFFRACTIONr_bond_other_d0.0010.021195
X-RAY DIFFRACTIONr_angle_refined_deg1.3591.9471753
X-RAY DIFFRACTIONr_angle_other_deg0.80632755
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8885162
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.48123.60761
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.08615228
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8411512
X-RAY DIFFRACTIONr_chiral_restr0.0740.2198
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021452
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02273
X-RAY DIFFRACTIONr_nbd_refined0.2260.2289
X-RAY DIFFRACTIONr_nbd_other0.1850.21148
X-RAY DIFFRACTIONr_nbtor_refined0.1820.2644
X-RAY DIFFRACTIONr_nbtor_other0.0820.2717
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2450.2123
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.2510.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1390.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3050.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3370.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0811.5883
X-RAY DIFFRACTIONr_mcbond_other0.2561.5335
X-RAY DIFFRACTIONr_mcangle_it1.4421290
X-RAY DIFFRACTIONr_scbond_it2.5753546
X-RAY DIFFRACTIONr_scangle_it3.64.5463
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→2.002 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.241 130 -
Rwork0.194 2201 -
obs-2201 99.11 %

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