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- PDB-8tat: CRYSTAL STRUCTURE OF R9A SPIN LABELED T4 LYSOZYME MUTANT K65R9A/R76R9A -

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Basic information

Entry
Database: PDB / ID: 8tat
TitleCRYSTAL STRUCTURE OF R9A SPIN LABELED T4 LYSOZYME MUTANT K65R9A/R76R9A
ComponentsEndolysin
KeywordsANTIMICROBIAL PROTEIN / HYDROLASE / NITROXIDE SPIN LABEL / EPR / MODIFIED CYSTEINE / ANTIMICROBIAL / BACTERIOLYTIC ENZYME / GLYCOSIDASE
Function / homology
Function and homology information


cytolysis / 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
Biological speciesEscherichia phage T4 (virus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsChen, M. / Hubbell, W.L. / Cascio, D.
Funding support United States, Hungary, 2items
OrganizationGrant numberCountry
Other privateJules Stein Professorship endowment United States
Hungarian National Research, Development and Innovation OfficeNKFI K 137793 Hungary
CitationJournal: Appl.Magn.Reson. / Year: 2024
Title: A Highly Ordered Nitroxide Side Chain for Distance Mapping and Monitoring Slow Structural Fluctuations in Proteins.
Authors: Chen, M. / Kalai, T. / Cascio, D. / Bridges, M.D. / Whitelegge, J.P. / Elgeti, M. / Hubbell, W.L.
History
DepositionJun 27, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7203
Polymers18,3211
Non-polymers3982
Water2,558142
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.390, 60.390, 95.430
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Endolysin


Mass: 18321.014 Da / Num. of mol.: 1 / Mutation: C54T, K65C, R76C, C97A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia phage T4 (virus) / Plasmid: PHSE5 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A7S9SVX7
#2: Chemical ChemComp-GFX / methyl 1-hydroxy-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrole-3-carboxylate, radical


Mass: 199.247 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C10H17NO3 / Source: (gene. exp.) Escherichia phage T4 (virus) / Gene: LYSOZYME / Plasmid: PHSE5 / Production host: Escherichia coli BL21 (bacteria) / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.63 Å3/Da / Density % sol: 53.3 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 2.35M DIBASIC POTASSIUM PHOSPHATE AND MONOBASIC SODIUM PHOSPHATE, 0.15M SODIUM CHLORIDE, 100mM 1,6-HEXANEDIOL, 3% 2-PROPANOL, PH 7.4, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Jul 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→52.3 Å / Num. obs: 50346 / % possible obs: 97.8 % / Redundancy: 10.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.082 / Rrim(I) all: 0.086 / Net I/σ(I): 16.04
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.6-1.640.96236270.8371.0111
1.64-1.690.83136290.8990.8721
1.69-1.730.64434720.9390.6761
1.73-1.790.55234220.9570.581
1.79-1.850.44533130.9690.4671
1.85-1.910.39130970.9820.411
1.91-1.980.25131010.9860.2631
1.98-2.060.17829980.9940.1861
2.06-2.160.13929490.9960.1461
2.16-2.260.11826760.9950.1241
2.26-2.380.10525310.9970.111
2.38-2.530.08925290.9970.0931
2.53-2.70.08323540.9970.0871
2.7-2.920.07321690.9970.0761
2.92-3.20.06420470.9980.0681
3.2-3.580.05918290.9980.0621
3.58-4.130.05415930.9980.0571
4.13-5.060.05113850.9990.0541
5.06-7.150.05410470.9980.0571
7.15-52.30.0475780.9990.0491

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XSCALE20210323data scaling
PHASER2.8.3phasing
XDS20210323data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→52.3 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2185 1330 5 %
Rwork0.1977 --
obs0.1988 26611 97.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→52.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1291 0 0 142 1433
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061327
X-RAY DIFFRACTIONf_angle_d0.8741811
X-RAY DIFFRACTIONf_dihedral_angle_d6.279187
X-RAY DIFFRACTIONf_chiral_restr0.046202
X-RAY DIFFRACTIONf_plane_restr0.007227
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.660.23091280.21912434X-RAY DIFFRACTION96
1.66-1.720.20361290.18592451X-RAY DIFFRACTION97
1.72-1.80.22541290.19782474X-RAY DIFFRACTION97
1.8-1.90.25991310.22752478X-RAY DIFFRACTION97
1.9-2.010.36591310.24432488X-RAY DIFFRACTION96
2.01-2.170.22081320.19422516X-RAY DIFFRACTION98
2.17-2.390.261310.22362488X-RAY DIFFRACTION96
2.39-2.730.25621360.20552589X-RAY DIFFRACTION100
2.73-3.440.20811380.20322611X-RAY DIFFRACTION100
3.44-52.30.16961450.1712752X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -25.3921 Å / Origin y: 11.6227 Å / Origin z: 9.4028 Å
111213212223313233
T0.1532 Å2-0.0038 Å20.0064 Å2-0.1333 Å20.0142 Å2--0.1679 Å2
L0.6993 °20.4063 °20.233 °2-1.2806 °20.4605 °2--1.7816 °2
S0.0159 Å °-0.0175 Å °0.0445 Å °0.068 Å °0.0113 Å °0.0658 Å °-0.0024 Å °-0.0365 Å °-0.0212 Å °
Refinement TLS groupSelection details: all

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