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- PDB-8s3m: LysTt72, a lytic endopeptidase from Thermus thermophilus MAT72 ph... -

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Basic information

Entry
Database: PDB / ID: 8s3m
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: 2.198 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
Water1,17165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint-60 kcal/mol
Surface area15360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.133, 60.985, 125.342
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.: 65 / 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: 2.12 Å3/Da / Density % sol: 42.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
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: 0.7749 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 28, 2023 / Details: focussing mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7749 Å / Relative weight: 1
ReflectionResolution: 2.198→15 Å / Num. obs: 17755 / % possible obs: 99.2 % / Redundancy: 6.5 % / CC1/2: 0.994 / Rrim(I) all: 0.264 / Rsym value: 0.243 / Net I/av σ(I): 8.36 / Net I/σ(I): 8.36
Reflection shellResolution: 2.198→2.33 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 1.65 / Num. unique obs: 2775 / CC1/2: 0.726 / Rrim(I) all: 1.602 / Rsym value: 1.478 / % possible all: 98.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.198→14.956 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.924 / WRfactor Rfree: 0.238 / WRfactor Rwork: 0.165 / SU B: 9.401 / SU ML: 0.219 / Average fsc free: 0.9401 / Average fsc work: 0.9554 / Cross valid method: FREE R-VALUE / ESU R: 0.316 / ESU R Free: 0.243
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2598 930 5.238 %Random
Rwork0.1874 16825 --
all0.191 ---
obs-17755 99.223 %-
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: 41.393 Å2
Baniso -1Baniso -2Baniso -3
1-4.192 Å20 Å20 Å2
2---1.167 Å20 Å2
3----3.025 Å2
Refinement stepCycle: LAST / Resolution: 2.198→14.956 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2796 0 53 65 2914
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0122923
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162671
X-RAY DIFFRACTIONr_angle_refined_deg1.6411.8133965
X-RAY DIFFRACTIONr_angle_other_deg0.5711.7656152
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7715344
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.36513
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.88710472
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.77910142
X-RAY DIFFRACTIONr_chiral_restr0.0780.2421
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023437
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02729
X-RAY DIFFRACTIONr_nbd_refined0.2170.2606
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2070.22558
X-RAY DIFFRACTIONr_nbtor_refined0.1930.21461
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0870.21561
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.2122
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0140.21
X-RAY DIFFRACTIONr_metal_ion_refined0.1420.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2260.216
X-RAY DIFFRACTIONr_nbd_other0.2360.246
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.260.23
X-RAY DIFFRACTIONr_mcbond_it3.7173.9821382
X-RAY DIFFRACTIONr_mcbond_other3.7173.9811382
X-RAY DIFFRACTIONr_mcangle_it5.6487.1431724
X-RAY DIFFRACTIONr_mcangle_other5.6527.1451725
X-RAY DIFFRACTIONr_scbond_it4.414.4381541
X-RAY DIFFRACTIONr_scbond_other4.3894.4311538
X-RAY DIFFRACTIONr_scangle_it6.8497.9482241
X-RAY DIFFRACTIONr_scangle_other6.8477.952242
X-RAY DIFFRACTIONr_lrange_it8.6440.3773337
X-RAY DIFFRACTIONr_lrange_other8.64140.3893337
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
2.198-2.2540.268610.34711560.34312630.9090.8796.35790.326
2.254-2.3140.341580.30611760.30812340.9080.9041000.288
2.314-2.3790.317590.29611340.29711930.9270.9181000.275
2.379-2.4510.378530.2511410.25511940.890.9381000.228
2.451-2.5290.327630.23310650.23811280.9370.9511000.209
2.529-2.6150.273650.23110620.23311290.950.95699.82290.201
2.615-2.7110.293590.2369940.2410540.9240.95699.90510.209
2.711-2.8170.262570.2019790.20510370.950.9799.90360.174
2.817-2.9380.293540.1959420.29960.940.9741000.169
2.938-3.0750.323570.1848880.1929450.9320.9751000.166
3.075-3.2340.362430.2068840.2139270.9320.9711000.181
3.234-3.420.265470.1928260.1968740.9520.97899.88560.174
3.42-3.6430.194500.1567560.1588090.9770.98799.62920.145
3.643-3.9150.211380.1537370.1567770.9720.98699.74260.142
3.915-4.260.177380.1296740.1327130.9780.9999.85970.121
4.26-4.7150.191440.1246260.1286700.9790.991000.119
4.715-5.3570.261240.1465680.1525950.9770.98799.49580.142
5.357-6.360.438230.1855070.1945320.9110.98199.62410.175
6.36-8.2770.208240.1654000.1684290.9580.98498.83450.166
8.277-14.9560.18130.1493100.153230.9830.9861000.161

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