[English] 日本語
Yorodumi
- PDB-7rum: Endolysin from Escherichia coli O157:H7 phage FTEbC1, LysT84 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7rum
TitleEndolysin from Escherichia coli O157:H7 phage FTEbC1, LysT84
ComponentsEndolysin
KeywordsHYDROLASE / Endolysin / peptidoglycan hydrolase / bacteriophage
Function / homologyN-acetylmuramidase / N-acetylmuramidase / PGBD superfamily / Peptidoglycan binding-like / Putative peptidoglycan binding domain / PGBD-like superfamily / Endolysin
Function and homology information
Biological speciesSalmonella phage GEC_vB_GOT (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 Å
AuthorsLove, M.J. / Billington, C. / Dobson, R.C.J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biochem.J. / Year: 2022
Title: The structure and function of modular Escherichia coli O157:H7 bacteriophage FTBEc1 endolysin, LysT84: defining a new endolysin catalytic subfamily.
Authors: Love, M.J. / Coombes, D. / Ismail, S. / Billington, C. / Dobson, R.C.J.
History
DepositionAug 17, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Endolysin
B: Endolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,8836
Polymers62,5152
Non-polymers3684
Water1,56787
1
A: Endolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4423
Polymers31,2571
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Endolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4423
Polymers31,2571
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)106.928, 106.928, 369.259
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6
Components on special symmetry positions
IDModelComponents
11A-442-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and ((resid 4 and (name N or name...
d_2ens_1(chain "B" and (resid 4 through 102 or (resid 103...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1LEUCYSA3 - 263
d_12ens_1GOLGOLB
d_13ens_1GOLGOLC
d_21ens_1LEUCYSD1 - 261
d_22ens_1GOLGOLE
d_23ens_1GOLGOLF

NCS oper: (Code: givenMatrix: (0.872399463877, -0.488645226443, -0.0120423461758), (-0.488789308071, -0.872230163196, -0.0173076493567), (-0.00204639733111, 0.0209853540746, -0.999777688875)Vector: - ...NCS oper: (Code: given
Matrix: (0.872399463877, -0.488645226443, -0.0120423461758), (-0.488789308071, -0.872230163196, -0.0173076493567), (-0.00204639733111, 0.0209853540746, -0.999777688875)
Vector: -13.7299008751, -53.3952271406, 30.5211066145)

-
Components

#1: Protein Endolysin


Mass: 31257.457 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella phage GEC_vB_GOT (virus) / Gene: GECvBGOT_gp079c / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A7S9SQH6
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 5.32 Å3/Da / Density % sol: 76.89 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: Morpheus I condition F3: 0.12 M monosaccharides [0.2 M D-glucose; 0.2 M D-mannose; 0.2 M D-galactose; 0.2 M L-fucose; 0.2 M D-xylose; 0.2 M N-acetyl-D-glucosamine] 0.1 M buffer System 1 [1.0 ...Details: Morpheus I condition F3: 0.12 M monosaccharides [0.2 M D-glucose; 0.2 M D-mannose; 0.2 M D-galactose; 0.2 M L-fucose; 0.2 M D-xylose; 0.2 M N-acetyl-D-glucosamine] 0.1 M buffer System 1 [1.0 M imidazole; MES monohydrate (acid) pH 6.5], 30% v/v Precipitant Mix 3 [40% v/v glycerol; 20% w/v PEG 4000

-
Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.99→49.04 Å / Num. obs: 26401 / % possible obs: 99.9 % / Redundancy: 18.5 % / CC1/2: 0.974 / Rmerge(I) obs: 0.521 / Rpim(I) all: 0.124 / Rrim(I) all: 0.535 / Net I/σ(I): 6.6 / Num. measured all: 487418 / Scaling rejects: 92
Reflection shell

Diffraction-ID: 1 / % possible all: 99.5

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs
2.99-3.1717.13.4037019841150.5540.8413.5091.1
8.97-49.04160.0921857311640.9710.0240.09519.7

-
Processing

Software
NameVersionClassification
PHENIX1.19-40refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NM7

5nm7


Resolution: 2.99→49.04 Å / SU ML: 0.3929 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 25.8838
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2722 1333 5.07 %
Rwork0.2326 24967 -
obs0.2346 26300 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.27 Å2
Refinement stepCycle: LAST / Resolution: 2.99→49.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3982 0 24 87 4093
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00244078
X-RAY DIFFRACTIONf_angle_d0.51875489
X-RAY DIFFRACTIONf_chiral_restr0.0362588
X-RAY DIFFRACTIONf_plane_restr0.0036715
X-RAY DIFFRACTIONf_dihedral_angle_d4.8405572
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.837109117449 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.99-3.10.36771460.32612374X-RAY DIFFRACTION99.17
3.1-3.220.35681210.2882444X-RAY DIFFRACTION99.96
3.22-3.370.31471190.27632464X-RAY DIFFRACTION100
3.37-3.550.31861400.26342424X-RAY DIFFRACTION100
3.55-3.770.2451220.21572468X-RAY DIFFRACTION100
3.77-4.060.22881320.20292466X-RAY DIFFRACTION100
4.06-4.470.2551270.18892506X-RAY DIFFRACTION100
4.47-5.110.22991300.20192519X-RAY DIFFRACTION100
5.11-6.440.26311370.25172557X-RAY DIFFRACTION100
6.44-49.040.27851590.23712745X-RAY DIFFRACTION99.93
Refinement TLS params.Method: refined / Origin x: -23.3299402913 Å / Origin y: -22.4033130523 Å / Origin z: 15.3999379554 Å
111213212223313233
T0.492319157485 Å2-0.068743535923 Å20.0298864400155 Å2-0.374155485416 Å20.00644330453844 Å2--0.36059261656 Å2
L0.171165469785 °20.416683425279 °2-0.0877904786441 °2-1.60845690596 °2-0.186628853267 °2--0.283921935736 °2
S-0.0338100869412 Å °-0.0404568563684 Å °-0.0557299424043 Å °-0.279243822295 Å °-0.0535423901427 Å °-0.00106583896971 Å °0.120704026267 Å °-0.145946171837 Å °0.0713956668813 Å °
Refinement TLS groupSelection details: all

+
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