[English] 日本語
Yorodumi
- PDB-8xem: Crystal structure of apo HEPN toxin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8xem
TitleCrystal structure of apo HEPN toxin
ComponentsHEPN
KeywordsTOXIN / ribonuclease
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsJin, C. / Jeon, C. / Kim, D.H. / Lee, B.J.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2018R1A5A2024425 Korea, Republic Of
National Research Foundation (NRF, Korea)2021R1F1A1050961 Korea, Republic Of
CitationJournal: To Be Published
Title: Structural and functional study of HEPN-MNT module from Legionella pneumophila
Authors: Jin, C. / Jeon, C. / Kim, D.H. / Lee, B.J.
History
DepositionDec 12, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 18, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HEPN
B: HEPN
C: HEPN
D: HEPN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,2466
Polymers65,1974
Non-polymers492
Water7,909439
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)143.880, 53.185, 86.965
Angle α, β, γ (deg.)90.000, 122.100, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

-
Components

#1: Protein
HEPN


Mass: 16299.340 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 439 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 43.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20% (w/v) PEG 3350, pH 6.5, 0.2 M ammonium tartrate dibasic

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.97942 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 24, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 51227 / % possible obs: 98.4 % / Redundancy: 6.7 % / Biso Wilson estimate: 25.19 Å2 / CC1/2: 0.994 / Net I/σ(I): 24.8
Reflection shellResolution: 1.8→1.83 Å / Num. unique obs: 2583 / CC1/2: 0.881

-
Processing

Software
NameVersionClassification
PHENIX1.20rc4_4418refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→48.75 Å / SU ML: 0.1714 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.3341
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2081 1980 3.91 %
Rwork0.1666 48701 -
obs0.1682 50681 97.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.52 Å2
Refinement stepCycle: LAST / Resolution: 1.8→48.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4334 0 2 439 4775
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00484423
X-RAY DIFFRACTIONf_angle_d0.78175951
X-RAY DIFFRACTIONf_chiral_restr0.0438627
X-RAY DIFFRACTIONf_plane_restr0.0071772
X-RAY DIFFRACTIONf_dihedral_angle_d4.7077565
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.840.25111180.19943289X-RAY DIFFRACTION92.81
1.84-1.890.29291500.20063424X-RAY DIFFRACTION95.74
1.89-1.950.24681220.19193427X-RAY DIFFRACTION96.89
1.95-2.010.24011630.18983446X-RAY DIFFRACTION97.36
2.01-2.080.23631380.17793445X-RAY DIFFRACTION96.45
2.08-2.170.19881390.16973505X-RAY DIFFRACTION98.14
2.17-2.260.21461520.15543498X-RAY DIFFRACTION98.46
2.26-2.380.19221260.163504X-RAY DIFFRACTION98.24
2.38-2.530.16821530.1563463X-RAY DIFFRACTION96.63
2.53-2.730.21771390.17463537X-RAY DIFFRACTION98.92
2.73-30.21251460.17813521X-RAY DIFFRACTION98.15
3-3.440.24811430.17453513X-RAY DIFFRACTION97.52
3.44-4.330.19321410.14923574X-RAY DIFFRACTION98.7
4.33-48.750.18211500.163555X-RAY DIFFRACTION96.16
Refinement TLS params.Method: refined / Origin x: 15.651245977 Å / Origin y: 14.3070700735 Å / Origin z: 19.7038938608 Å
111213212223313233
T0.171192352665 Å20.012637510922 Å2-0.00842984073582 Å2-0.153363115947 Å2-0.0294381877305 Å2--0.142907953062 Å2
L1.74784103223 °20.229164901747 °2-0.0721534031225 °2-0.402644054794 °2-0.150632920376 °2--0.4596245778 °2
S0.0141350791473 Å °-0.114637090565 Å °-0.0937864007354 Å °-0.0438620711137 Å °0.0111731011016 Å °-0.0438189344287 Å °0.0377189798396 Å °0.0275627387376 Å °-0.0257178222691 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