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- PDB-5xpe: Neutron structure of the T26H mutant of T4 lysozyme -

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Basic information

Entry
Database: PDB / ID: 5xpe
TitleNeutron structure of the T26H mutant of T4 lysozyme
ComponentsEndolysinLysin
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
Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / Lysozyme-like domain superfamily
Similarity search - Domain/homology
DEUTERATED WATER / Endolysin / Endolysin
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / NEUTRON DIFFRACTION / SYNCHROTRON / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 1.648 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 1.1Oct 11, 2017Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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)18,7955
Polymers18,6651
Non-polymers1294
Water1,54986
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area510 Å2
ΔGint-35 kcal/mol
Surface area8790 Å2
Unit cell
Length a, b, c (Å)61.230, 61.230, 96.791
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 18665.406 Da / Num. of mol.: 1 / Mutation: T26H
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
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-DOD / water / Heavy water


Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: D2O

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Experimental details

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Experiment

Experiment
MethodNumber of used crystals
X-RAY DIFFRACTION1
NEUTRON DIFFRACTION1

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Sample preparation

CrystalDensity Matthews: 2.81 Å3/Da / Density % sol: 56.17 %
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

Diffraction
IDMean temperature (K)Crystal-ID
12931
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL26B111
NUCLEAR REACTORORNL High Flux Isotope Reactor CG4D23.3-4.5
Detector
TypeIDDetectorDate
RAYONIX MX225HE1CCDMay 11, 2015
MAATEL IMAGINE2IMAGE PLATEDec 17, 2014
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111) double crystalSINGLE WAVELENGTHMx-ray2
2LAUELneutron1
Radiation wavelength
IDWavelength (Å)Relative weight
111
23.31
34.51
Reflection

Entry-ID: 5XPE

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)Rmerge(I) obsRpim(I) allRrim(I) allRsym valueΧ2Diffraction-IDNet I/σ(I)
1.648-46.5052592799.910.80.0530.0180.0570.0532.037165.2
2.099-17.1071010879.83.20.2220.1230.2560.22224.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allRsym valueΧ2Diffraction-ID% possible all
1.65-1.718.50.5275.325380.9170.1920.5620.5271.1381100
2.1-2.212.60.3322.20.2110.3960.332268.3
2.21-2.352.90.3372.10.1960.3930.337271.6
2.35-2.5130.322.10.1850.3720.32273.9
2.51-2.712.80.3052.20.1870.360.305278.7
2.71-2.972.90.2632.60.1590.3090.263278.6
2.97-3.323.10.2452.80.1440.2860.245284.6
3.32-3.833.50.2143.10.1170.2450.214291.5
3.83-4.74.10.1933.20.0970.2170.193295.6
4.7-6.644.20.1733.40.0860.1950.173295.8
6.64-17.10730.0965.50.0580.1130.096286

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Processing

Software
NameVersionClassification
LAUEGENdata processing
SCALA3.2.25data scaling
PDB_EXTRACT3.22data extraction
PHENIX1.9_1692refinement
Cootmodel building
Refinement

R Free selection details: Random selection / Cross valid method: FREE R-VALUE / Method to determine structure: MOLECULAR REPLACEMENT / Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Starting model: 1QT8

1qt8

Resolution (Å)Refine-IDBiso max (Å2)Biso mean (Å2)Biso min (Å2)Rfactor RfreeRfactor RworkRfactor obsNum. reflection RfreeNum. reflection obs% reflection Rfree (%)% reflection obs (%)SU MLDiffraction-IDσ(F)Phase error
1.648-46.505X-RAY DIFFRACTION122.9839.7116.960.18460.1550.15651303258885.0399.680.1511.3519.03
2.09-17.025NEUTRON DIFFRACTION0.2780.22470.2275513101075.0878.350.392030.68
Refinement stepCycle: final / Resolution: 1.648→46.505 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1312 0 5 203 1520
Biso mean--43.3 48.06 -
Num. residues----164
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0163169
X-RAY DIFFRACTIONf_angle_d1.4325575
X-RAY DIFFRACTIONf_chiral_restr0.09220
X-RAY DIFFRACTIONf_plane_restr0.008487
X-RAY DIFFRACTIONf_dihedral_angle_d18.092879
LS refinement shell

Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-IDNum. reflection allTotal num. of bins used% reflection obs (%)
1.6482-1.71420.26971370.21362636X-RAY DIFFRACTION2773998
1.7142-1.79220.24861440.20522720X-RAY DIFFRACTION28649100
1.7922-1.88670.21281450.18792661X-RAY DIFFRACTION28069100
1.8867-2.00490.17941420.17942725X-RAY DIFFRACTION28679100
2.0049-2.15970.20181450.16772719X-RAY DIFFRACTION28649100
2.1597-2.3770.19191410.16122726X-RAY DIFFRACTION28679100
2.377-2.7210.19791510.16642734X-RAY DIFFRACTION28859100
2.721-3.4280.22441440.16582791X-RAY DIFFRACTION29359100
3.428-46.52360.15221540.13382873X-RAY DIFFRACTION3027999
2.0899-2.29980.43921030.32432042NEUTRON DIFFRACTION2145468
2.2998-2.63150.30851250.28482238NEUTRON DIFFRACTION2363475
2.6315-3.31140.32451270.22632398NEUTRON DIFFRACTION2525479
3.3114-17.02530.19691580.16262916NEUTRON DIFFRACTION3074491

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