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- PDB-8s3u: LysTt72, a lytic endopeptidase from Thermus thermophilus MAT72 ph... -

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Basic information

Entry
Database: PDB / ID: 8s3u
TitleLysTt72, a lytic endopeptidase from Thermus thermophilus MAT72 phage vB_Tt72
Components
  • Lytic endopeptidase
  • gamma-D-Glu-m-A2pm-L-Lys-L-Arg
KeywordsVIRAL PROTEIN / Endopeptidase / Metalloprotein / Thermostability / Bacteriophage
Function / homologyPHOSPHATE ION
Function and homology information
Biological speciesThermus phage Tt72 (virus)
Escherichia coli BL21 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.301 Å
AuthorsRypniewski, W. / Biniek-Antosiak, K. / Bejger, M.
Funding support Poland, 1items
OrganizationGrant numberCountry
Other governmentUMO-2019/34/H/NZ2/00584 Poland
CitationJournal: J.Struct.Biol. / Year: 2025
Title: Crystal structure, enzymatic and thermodynamic properties of the Thermus thermophilus phage Tt72 lytic endopeptidase with unique structural signatures of thermal adaptation.
Authors: Dorawa, S. / Biniek-Antosiak, K. / Bejger, M. / Kaczorowska, A.K. / Ciuchcinski, K. / Godlewska, A. / Plotka, M. / Hreggvidsson, G.O. / Dziewit, L. / Kaczorowski, T. / Rypniewski, W.
History
DepositionFeb 20, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 5, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 17, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lytic endopeptidase
C: gamma-D-Glu-m-A2pm-L-Lys-L-Arg
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6075
Polymers40,3522
Non-polymers2553
Water37821
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint-62 kcal/mol
Surface area14900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.530, 60.150, 124.250
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Lytic endopeptidase


Mass: 39745.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus phage Tt72 (virus) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): BL21(DE3)[pRARE] / References: EC: 3.4.24.32
#2: Protein/peptide gamma-D-Glu-m-A2pm-L-Lys-L-Arg


Mass: 605.684 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BL21(DE3) (bacteria)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 1.88 Å3/Da / Density % sol: 34.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 20% v/v PEG 500 MME, 10% w/v PEG 20000, 30 mM sodium nitrate, 30 mM sodium phosphate dibasic, 30 mM ammonium sulfate, 0.1 M 6.5 imidazole/MES monohydrate (acid) at pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: cold nitrogen gas jet / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 8, 2023 / Details: focussing mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.3→100 Å / Num. obs: 14096 / % possible obs: 99.9 % / Redundancy: 13 % / CC1/2: 0.999 / Rmerge(I) obs: 0.107 / Rrim(I) all: 0.111 / Net I/σ(I): 13.58
Reflection shellResolution: 2.3→2.44 Å / Redundancy: 12 % / Mean I/σ(I) obs: 1.42 / Num. unique obs: 2197 / CC1/2: 0.848 / Rrim(I) all: 1.725 / Rsym value: 1.652 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.301→62.125 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.912 / SU B: 13.593 / SU ML: 0.3 / Cross valid method: FREE R-VALUE / ESU R: 0.532 / ESU R Free: 0.32
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2976 564 4.003 %
Rwork0.1927 13526 -
all0.197 --
obs-14090 99.879 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 72.882 Å2
Baniso -1Baniso -2Baniso -3
1-5.509 Å20 Å20 Å2
2--1.456 Å2-0 Å2
3----6.965 Å2
Refinement stepCycle: LAST / Resolution: 2.301→62.125 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2837 0 11 21 2869
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0122919
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162670
X-RAY DIFFRACTIONr_angle_refined_deg1.9091.8133957
X-RAY DIFFRACTIONr_angle_other_deg0.6321.7656150
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3585344
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.628513
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.0610472
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.19710142
X-RAY DIFFRACTIONr_chiral_restr0.0840.2420
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023437
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02729
X-RAY DIFFRACTIONr_nbd_refined0.2390.2686
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2150.22747
X-RAY DIFFRACTIONr_nbtor_refined0.2020.21484
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.090.21559
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2610.2118
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0120.22
X-RAY DIFFRACTIONr_metal_ion_refined0.2090.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1590.233
X-RAY DIFFRACTIONr_nbd_other0.2290.293
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1020.26
X-RAY DIFFRACTIONr_mcbond_it7.6877.0711382
X-RAY DIFFRACTIONr_mcbond_other7.6837.0691382
X-RAY DIFFRACTIONr_mcangle_it10.46612.6791724
X-RAY DIFFRACTIONr_mcangle_other10.47812.6811725
X-RAY DIFFRACTIONr_scbond_it8.4897.6261537
X-RAY DIFFRACTIONr_scbond_other8.4697.6151534
X-RAY DIFFRACTIONr_scangle_it12.32913.7312233
X-RAY DIFFRACTIONr_scangle_other12.32713.7332234
X-RAY DIFFRACTIONr_lrange_it15.95876.9593445
X-RAY DIFFRACTIONr_lrange_other15.95676.9633446
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.301-2.360.37410.4069580.40510080.8970.84699.10710.395
2.36-2.4250.498400.3769620.38110020.7970.8661000.36
2.425-2.4950.324420.3599110.3579540.9120.87599.89520.343
2.495-2.5720.394540.3338840.3369380.8850.8951000.306
2.572-2.6560.305280.2559020.2579300.910.9431000.23
2.656-2.7490.323330.2118480.2158810.9140.9661000.188
2.749-2.8520.293330.1918160.1958500.9560.97499.88240.17
2.852-2.9690.353330.1918000.1978340.940.97499.88010.169
2.969-3.10.365320.1757570.1827890.8790.9781000.154
3.1-3.2510.311280.1737290.187570.9310.9791000.156
3.251-3.4270.245320.1447060.1497380.9640.9851000.127
3.427-3.6340.285250.1516700.1556960.9610.98599.85630.139
3.634-3.8840.306230.1556140.1596370.9460.9841000.15
3.884-4.1940.277260.1555890.166150.9430.9831000.155
4.194-4.5920.209250.1395530.1425780.9730.9881000.145
4.592-5.130.311200.1624940.1675140.9520.9851000.178
5.13-5.9170.255160.1924480.1944640.9660.981000.2
5.917-7.230.293120.1973830.23960.9530.97399.74750.211
7.23-10.1570.33150.183110.1853260.9470.981000.212
10.157-62.1250.27160.2671910.2671970.9520.9581000.334

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