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- PDB-5xpf: High-resolution X-ray structure of the T26H mutant of T4 lysozyme -

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Basic information

Entry
Database: PDB / ID: 5xpf
TitleHigh-resolution X-ray structure of the T26H mutant of T4 lysozyme
ComponentsEndolysin
KeywordsHYDROLASE / Alpha and beta protein / T26H mutant / Perdeuterated protein
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
HEXANE-1,6-DIOL / Endolysin / Endolysin
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.04 Å
AuthorsHiromoto, T. / Kuroki, R.
CitationJournal: Protein Sci. / Year: 2017
Title: Neutron structure of the T26H mutant of T4 phage lysozyme provides insight into the catalytic activity of the mutant enzyme and how it differs from that of wild type.
Authors: Hiromoto, T. / Meilleur, F. / Shimizu, R. / Shibazaki, C. / Adachi, M. / Tamada, T. / Kuroki, R.
History
DepositionJun 1, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 4, 2017Provider: repository / Type: Initial release
Revision 2.0Oct 11, 2017Group: Polymer sequence / Category: entity_poly / Item: _entity_poly.pdbx_target_identifier
Revision 2.1Nov 15, 2017Group: Refinement description / Category: pdbx_refine / refine / Item: _refine.pdbx_R_Free_selection_details
Revision 2.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,66116
Polymers18,6651
Non-polymers99515
Water4,360242
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2330 Å2
ΔGint-49 kcal/mol
Surface area9100 Å2
Unit cell
Length a, b, c (Å)59.839, 59.839, 95.828
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 18665.406 Da / Num. of mol.: 1 / Mutation: T26H, C54T, C97A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Gene: e, T4Tp126 / Plasmid: pET24 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: D9IEF7, UniProt: P00720*PLUS, lysozyme

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Non-polymers , 5 types, 257 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-HEZ / HEXANE-1,6-DIOL


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 242 / 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: 2.65 Å3/Da / Density % sol: 53.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Sodium-potassium phosphate, Sodium chloride, 1,6-Hexanediol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.8 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 30, 2014
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.04→50 Å / Num. obs: 95774 / % possible obs: 99.9 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.041 / Rpim(I) all: 0.019 / Rrim(I) all: 0.045 / Rsym value: 0.041 / Χ2: 2.263 / Net I/av σ(I): 51.6 / Net I/σ(I): 51.6
Reflection shellResolution: 1.04→1.08 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.361 / Mean I/σ(I) obs: 4.7 / Num. unique obs: 9481 / CC1/2: 0.886 / Rpim(I) all: 0.215 / Rrim(I) all: 0.422 / Rsym value: 0.361 / Χ2: 1.732 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data processing
HKL-2000data scaling
PDB_EXTRACT3.22data extraction
SHELXLrefinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QT8

1qt8


Resolution: 1.04→45.58 Å / Cross valid method: FREE R-VALUE / σ(F): 0 / Details: ANISOTROPIC REFINEMENT REDUCED FREE R
RfactorNum. reflection% reflectionSelection details
Rfree0.193 4786 5 %Random selection
Rwork0.159 ---
obs-95670 99.9 %-
Displacement parametersBiso max: 96.95 Å2 / Biso mean: 18.1199 Å2 / Biso min: 7.69 Å2
Refinement stepCycle: final / Resolution: 1.04→45.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1312 0 59 262 1633
Biso mean--35.2 28.61 -
Num. residues----164
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.012
X-RAY DIFFRACTIONs_angle_d0.029
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.004
X-RAY DIFFRACTIONs_zero_chiral_vol0.025
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.359
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.03
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.04
X-RAY DIFFRACTIONs_approx_iso_adps0

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