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- PDB-2hum: Crystal structure of T4 Lysozyme D72C synthetic dimer -

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Basic information

Entry
Database: PDB / ID: 2hum
TitleCrystal structure of T4 Lysozyme D72C 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 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 2 CHAINS. ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAINS. SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE. THE BIOLOGICAL UNIT IS A DIMER FORMED BY DISULFIDE BOND BETWEEN CYSTEINES 72. THE DIMER IS PRESENT ENTIRELY IN THE ASYMMETRIC UNIT AND DOES NOT HAVE A CRYSTALLOGRAPHIC SYMMETRY.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lysozyme
B: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3553
Polymers37,2332
Non-polymers1221
Water1,78399
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.306, 55.907, 80.292
Angle α, β, γ (deg.)90.00, 108.13, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 18616.418 Da / Num. of mol.: 2 / Mutation: C54T, D72C, 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 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P00720, lysozyme
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 3.17 Å3/Da / Density % sol: 61.17 %
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 / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2 M tri-Lithium Citrate, 20% PEG 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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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: Feb 2, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→76.25 Å / Num. obs: 27769 / % possible obs: 99.5 % / Observed criterion σ(F): 2
Reflection shellResolution: 2.1→2.18 Å / % possible all: 98.8

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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: 2.35→52.6 Å / Cor.coef. Fo:Fc: 0.891 / Cor.coef. Fo:Fc free: 0.839 / SU B: 14.465 / SU ML: 0.184 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.341 / ESU R Free: 0.278 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DATA WAS COLLECTED TO 2.10 ANGSTROM RESOLUTION. STRUCTURE WAS REFINED TO 2.35 ANGSTROM RESOLUTION.
RfactorNum. reflection% reflectionSelection details
Rfree0.30355 993 5.1 %RANDOM
Rwork0.23939 ---
obs0.24277 18576 99.67 %-
all-19569 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.3 Å2
Baniso -1Baniso -2Baniso -3
1-1.11 Å20 Å20.63 Å2
2---1.86 Å20 Å2
3---1.14 Å2
Refinement stepCycle: LAST / Resolution: 2.35→52.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2612 0 8 99 2719
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0222660
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.081.9563583
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1285326
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.82523.387124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.10615496
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4621526
X-RAY DIFFRACTIONr_chiral_restr0.1330.2400
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021968
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2260.21285
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.21812
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1970.2154
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2970.231
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1930.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4781.51721
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.95422606
X-RAY DIFFRACTIONr_scbond_it3.51431149
X-RAY DIFFRACTIONr_scangle_it5.0754.5977
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 76 -
Rwork0.215 1351 -
obs--99.44 %

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