[English] 日本語
Yorodumi
- PDB-7vkb: Crystal structure of the a bacterial kinase complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7vkb
TitleCrystal structure of the a bacterial kinase complex
Components
  • HipA (Persistence to inhibition of murein or DNA biosynthesis)
  • HipA_C domain-containing protein
KeywordsTOXIN/ANTITOXIN / TOXIN ANTITOXIN SYSTEM / TOXIN / TOXIN-ANTITOXIN complex
Function / homologyHipA, N-terminal subdomain 1 / HipA N-terminal domain / HipA-like, C-terminal / HipA-like C-terminal domain / transferase activity / DI(HYDROXYETHYL)ETHER / HipA-like C-terminal domain-containing protein / HipA (Persistence to inhibition of murein or DNA biosynthesis)
Function and homology information
Biological speciesLegionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.82 Å
AuthorsZhen, X. / Ouyang, S.Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32170045 China
CitationJournal: Nat Commun / Year: 2022
Title: Molecular mechanism of toxin neutralization in the HipBST toxin-antitoxin system of Legionella pneumophila.
Authors: Zhen, X. / Wu, Y. / Ge, J. / Fu, J. / Ye, L. / Lin, N. / Huang, Z. / Liu, Z. / Luo, Z.Q. / Qiu, J. / Ouyang, S.
History
DepositionSep 29, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 29, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HipA_C domain-containing protein
B: HipA (Persistence to inhibition of murein or DNA biosynthesis)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7964
Polymers48,6672
Non-polymers1292
Water4,378243
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2440 Å2
ΔGint-13 kcal/mol
Surface area17620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.220, 45.220, 394.550
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-529-

HOH

-
Components

#1: Protein HipA_C domain-containing protein


Mass: 36957.707 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)
Gene: lpg2370
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q5ZSZ6
#2: Protein HipA (Persistence to inhibition of murein or DNA biosynthesis)


Mass: 11709.013 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)
Gene: lpg2369 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5ZSZ7
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 243 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.64 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.2 / Details: 0.1M Sodium acetate PH 7.0 12% PEG 3350 / PH range: 6-8

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97981 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 30, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97981 Å / Relative weight: 1
ReflectionResolution: 1.82→31.871 Å / Num. obs: 38842 / % possible obs: 100 % / Redundancy: 15.1 % / Biso Wilson estimate: 38.79 Å2 / CC1/2: 1 / Net I/σ(I): 2
Reflection shellResolution: 1.82→1.87 Å / Rmerge(I) obs: 0.089 / Num. unique obs: 2774 / CC1/2: 0.801 / Rpim(I) all: 0.091 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.82→31.87 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.246 1894 4.9 %
Rwork0.2047 36766 -
obs0.2068 38660 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 160.45 Å2 / Biso mean: 46.2556 Å2 / Biso min: 27.28 Å2
Refinement stepCycle: final / Resolution: 1.82→31.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2924 0 8 243 3175
Biso mean--62.32 49.3 -
Num. residues----363
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.82-1.870.32511200.269225472667
1.87-1.920.33021220.248725642686
1.92-1.970.29651480.229825642712
1.97-2.040.27871340.226425432677
2.04-2.110.24071070.226425972704
2.11-2.190.21271480.203125662714
2.19-2.290.22951290.208725972726
2.29-2.410.25521460.210925652711
2.41-2.560.24271190.214726262745
2.56-2.760.28911440.224626092753
2.76-3.040.26491390.215126562795
3.04-3.480.23991290.208427002829
3.48-4.380.211420.173226902832
4.38-31.870.25411670.206929423109
Refinement TLS params.Method: refined / Origin x: 25.8055 Å / Origin y: 18.4674 Å / Origin z: 73.6968 Å
111213212223313233
T0.1351 Å20.0188 Å20.0224 Å2-0.2203 Å2-0.0262 Å2--0.223 Å2
L1.1208 °20.3686 °20.5591 °2-0.665 °2-0.0297 °2--2.1078 °2
S0.0754 Å °-0.0319 Å °0.1227 Å °0.0891 Å °-0.0836 Å °0.0081 Å °0.1117 Å °-0.1821 Å °-0.0032 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA52 - 312
2X-RAY DIFFRACTION1allB1 - 102
3X-RAY DIFFRACTION1allC1
4X-RAY DIFFRACTION1allD1
5X-RAY DIFFRACTION1allS1 - 243

+
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