[English] 日本語
Yorodumi
- PDB-8s3u: LysTt72, a lytic endopeptidase from Thermus thermophilus MAT72 ph... -

+
Open data


ID or keywords:

Loading...

-
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: To be published
Title: LysTt72, a lytic endopeptidase from Thermus thermophilus MAT72 phage vB_Tt72
Authors: Rypniewski, W. / Biniek-Antosiak, K. / Bejger, M.
History
DepositionFeb 20, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 5, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more