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- PDB-2huk: Crystal structure of T4 Lysozyme V131C synthetic dimer -

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Basic information

Entry
Database: PDB / ID: 2huk
TitleCrystal structure of T4 Lysozyme V131C synthetic dimer
ComponentsLysozyme
KeywordsHYDROLASE / T4 Lysozyme synthetic dimer
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: 2 Å
AuthorsBanatao, D.R. / Cascio, D. / Yeates, T.O.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: An approach to crystallizing proteins by synthetic symmetrization.
Authors: Banatao, D.R. / Cascio, D. / Crowley, C.S. / Fleissner, M.R. / Tienson, H.L. / Yeates, T.O.
History
DepositionJul 26, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 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 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE. THE BIOLOGICAL UNIT IS A DIMER FORMED BY DISULFIDE BOND BETWEEN CYSTEINES 131. THE DISULFIDE BOND OVERLAPS WITH THE CRYSTALLOGRAPHIC 2-FOLD AXIS. THE DIMER IS A SYMMETRICAL DIMER.

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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)19,0175
Polymers18,6321
Non-polymers3844
Water1,69394
1
A: Lysozyme
hetero molecules

A: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,03310
Polymers37,2652
Non-polymers7698
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Unit cell
Length a, b, c (Å)184.267, 29.408, 31.243
Angle α, β, γ (deg.)90.00, 97.39, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 18632.375 Da / Num. of mol.: 1 / Mutation: V131C
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 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P00720, lysozyme
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Mutation: C54T / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 94 / Mutation: C97A / 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: 2.27 Å3/Da / Density % sol: 45.9 %
Description: Terminal residues 163 and 164 for T4 lysozyme have poor electron density. This should be taken into account when using this structure as a model.
Crystal growTemperature: 295 K / pH: 6.5
Details: 20% PEG 8000, 0.1M Na Cacodylate, pH 6.5, 0.2M Ammonium Acetate, VAPOR DIFFUSION, HANGING DROP, temperature 295K, pH 6.50

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 26, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→25 Å / Num. obs: 15287 / % possible obs: 96.8 % / Observed criterion σ(F): 2 / Rsym value: 0.068 / Net I/σ(I): 14.3
Reflection shellResolution: 1.8→1.86 Å / Mean I/σ(I) obs: 2.05 / Rsym value: 0.445 / % possible all: 93.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1C6T

1c6t


Resolution: 2→25 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.892 / SU B: 7.058 / SU ML: 0.106 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.195 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24 567 5 %RANDOM
Rwork0.178 ---
obs0.181 10730 97.8 %-
all-11299 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.05 Å2
Baniso -1Baniso -2Baniso -3
1-0.63 Å20 Å20.27 Å2
2---1.03 Å20 Å2
3---0.48 Å2
Refinement stepCycle: LAST / Resolution: 2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1316 0 20 94 1430
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0221355
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7151.971830
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9375167
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.55723.49263
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.32415251
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2831513
X-RAY DIFFRACTIONr_chiral_restr0.1270.2203
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02996
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2260.2674
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2970.2935
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1910.280
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.360.244
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1580.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2161.5857
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.75421312
X-RAY DIFFRACTIONr_scbond_it3.4373588
X-RAY DIFFRACTIONr_scangle_it5.0154.5516
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 46 -
Rwork0.189 774 -
obs--97.27 %

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