[English] 日本語
Yorodumi
- PDB-1gvn: Crystal Structure of the Plasmid Maintenance System epsilon/zeta:... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1gvn
TitleCrystal Structure of the Plasmid Maintenance System epsilon/zeta: Meachnism of toxin inactivation and toxin function
Components
  • EPSILON
  • ZETA
KeywordsPOSTSEGREGATIONAL KILLING SYSTEM / PLASMID
Function / homology
Function and homology information


negative regulation of cell killing / UDP-N-acetylglucosamine kinase / toxic substance binding / response to toxic substance / kinase activity / phosphorylation / ATP binding
Similarity search - Function
Bacterial epsilon antitoxin / Bacterial epsilon antitoxin / Helicase, Ruva Protein; domain 3 - #130 / Antitoxin epsilon/PezA domain superfamily / Zeta toxin domain / Zeta toxin / Helicase, Ruva Protein; domain 3 / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold ...Bacterial epsilon antitoxin / Bacterial epsilon antitoxin / Helicase, Ruva Protein; domain 3 - #130 / Antitoxin epsilon/PezA domain superfamily / Zeta toxin domain / Zeta toxin / Helicase, Ruva Protein; domain 3 / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Toxin zeta / Antitoxin epsilon
Similarity search - Component
Biological speciesSTREPTOCOCCUS PYOGENES (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.95 Å
AuthorsMeinhart, A. / Alonso, J.C. / Straeter, N. / Saenger, W.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: Crystal Structure of the Plasmid Maintenance System Epsilon /Zeta : Functional Mechanism of Toxin Zeta and Inactivation by Epsilon 2 Zeta 2 Complex Formation
Authors: Meinhart, A. / Alonso, J.C. / Strater, N. / Saenger, W.
History
DepositionFeb 19, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 29, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: EPSILON
B: ZETA
C: EPSILON
D: ZETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,5506
Polymers86,3584
Non-polymers1922
Water12,538696
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)59.236, 79.847, 191.439
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.19973, 0.76907, 0.60715), (0.7701, -0.50633, 0.38803), (0.60585, 0.39007, -0.69339)-43.39098, 35.16201, 41.26033
2given(0.21431, 0.77442, 0.59526), (0.77824, -0.50366, 0.37506), (0.59027, 0.38288, -0.71063)-43.33834, 35.29405, 42.00922
DetailsTHE TETRAMERIC ASSEMBLY CONSISTS OF 2 HETERO DIMERS OFEPSILON AND ZETA (A,C AND B,D)

-
Components

#1: Protein EPSILON /


Mass: 10734.217 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: ENCODED ON PLASMID PSM19035 / Source: (natural) STREPTOCOCCUS PYOGENES (bacteria) / References: UniProt: Q57231
#2: Protein ZETA


Mass: 32444.969 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: ENCODED ON PLASMID PSM19035 / Source: (natural) STREPTOCOCCUS PYOGENES (bacteria) / References: UniProt: Q54944
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 696 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.75 Å3/Da / Density % sol: 48 %
Crystal growpH: 7 / Details: pH 7.00
Crystal grow
*PLUS
Temperature: 291 K / pH: 7.5 / Method: vapor diffusion, hanging drop / Details: Meinhart, A., (2001) Acta Crystallogr., D57, 745.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
18 mg/mlprotein1drop
250 mMTris-HCl1droppH7.5
35 mMdithiothreitol1drop
4100 mMsodium acetate1reservoirpH4.6
516 %(w/v)PEG33501reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 1.01629
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 3, 2000 / Details: TOROIDAL MIRROR
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.01629 Å / Relative weight: 1
ReflectionResolution: 1.95→19.96 Å / Num. obs: 64215 / % possible obs: 95.5 % / Redundancy: 5 % / Biso Wilson estimate: 8 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 15.5
Reflection shellResolution: 1.95→2 Å / Redundancy: 4 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 5.14 / % possible all: 91.8

-
Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEV. 1.17phasing
RefinementMethod to determine structure: MAD / Resolution: 1.95→19.96 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF
RfactorNum. reflection% reflectionSelection details
Rfree0.237 3157 5.1 %RANDOM
Rwork0.2 ---
obs0.2 62259 92.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.7859 Å2 / ksol: 0.338413 e/Å3
Displacement parametersBiso mean: 21 Å2
Baniso -1Baniso -2Baniso -3
1-2.34 Å20 Å20 Å2
2--0.89 Å20 Å2
3----3.23 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 1.95→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5776 0 10 696 6482
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.73
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.271.5
X-RAY DIFFRACTIONc_mcangle_it1.922
X-RAY DIFFRACTIONc_scbond_it2.112
X-RAY DIFFRACTIONc_scangle_it3.122.5
LS refinement shellResolution: 1.95→2.07 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.275 476 4.9 %
Rwork0.214 9154 -
obs--87.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor obs: 0.2 / Rfactor Rfree: 0.235 / Rfactor Rwork: 0.199
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.11
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.73

+
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