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- PDB-2hul: Crystal structure of T4 Lysozyme S44C synthetic dimer -

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Basic information

Entry
Database: PDB / ID: 2hul
TitleCrystal structure of T4 Lysozyme S44C 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 / Phage lysozyme / Lysozyme domain superfamily / Lysozyme / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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: Derived calculations / 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
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
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 44. 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)19,3058
Polymers18,6441
Non-polymers6617
Water2,522140
1
A: Lysozyme
hetero molecules

A: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,61016
Polymers37,2892
Non-polymers1,32114
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area3240 Å2
ΔGint-129 kcal/mol
Surface area16860 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)92.598, 28.926, 88.814
Angle α, β, γ (deg.)90.00, 119.42, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 18644.428 Da / Num. of mol.: 1 / Mutation: S44C
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


Mass: 96.063 Da / Num. of mol.: 4 / Mutation: C54T / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Mutation: C97A / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 2.78 Å3/Da / Density % sol: 55.72 %
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: 298 K / pH: 6.7
Details: 2.0 M Ammonium Sulfate, 0.1 M Cacodylate pH 6.7, 0.2 M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 6.70

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: May 26, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→77.38 Å / Num. obs: 19413 / % possible obs: 99.1 % / Rsym value: 0.056 / Net I/σ(I): 17.6
Reflection shellResolution: 1.5→1.55 Å / Mean I/σ(I) obs: 4.2 / Rsym value: 0.302 / % possible all: 94.1

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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: 1.8→40.32 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.048 / SU ML: 0.066 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.114 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DIFFERENCE MAPS SHOW THAT DISULFIDE BONDS ARE PARTIALLY BROKEN DUE TO SYNCHOTRON RADIATION. THE PRESENCE OF DISULFIDE BONDS WAS CONFIRMED ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DIFFERENCE MAPS SHOW THAT DISULFIDE BONDS ARE PARTIALLY BROKEN DUE TO SYNCHOTRON RADIATION. THE PRESENCE OF DISULFIDE BONDS WAS CONFIRMED BY GEL ELECTROPHORESIS AND CHROMATOGRAPHY PRIOR TO CRYSTALLIZATION. FOR MORE INFORMATION ON THIS PHENOMENON WE REFER TO: BANUMATHI ET AL. "STRUCTURAL EFFECTS OF RADIATION DAMAGE AND ITS POTENTIAL FOR PHASING", ACTA CRYST.(D60),1085-93,2004.
RfactorNum. reflection% reflectionSelection details
Rfree0.192 998 5.1 %RANDOM
Rwork0.178 ---
obs0.179 18415 99.8 %-
all-19413 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.78 Å2
Baniso -1Baniso -2Baniso -3
1-0.6 Å20 Å2-0.18 Å2
2---0.61 Å20 Å2
3----0.17 Å2
Refinement stepCycle: LAST / Resolution: 1.8→40.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1308 0 38 140 1486
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221386
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3591.9761866
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7335168
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.15323.38565
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.25615254
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4031514
X-RAY DIFFRACTIONr_chiral_restr0.0880.2204
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021013
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2010.2654
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.2951
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2106
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3440.242
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1110.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.111.5860
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.55921325
X-RAY DIFFRACTIONr_scbond_it2.6873606
X-RAY DIFFRACTIONr_scangle_it4.1474.5540
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.211 63 -
Rwork0.197 1329 -
obs--99.93 %

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