[English] 日本語
Yorodumi
- PDB-6eph: Structure of the epsilon_1 / zeta_1 antitoxin toxin system from N... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6eph
TitleStructure of the epsilon_1 / zeta_1 antitoxin toxin system from Neisseria gonorrhoeae in complex with UNAM.
Components
  • Epsilon_1 antitoxin
  • Zeta_1 toxin
KeywordsTOXIN / bacterial toxin antitoxin systems / small molecule kinases
Function / homology
Function and homology information


kinase activity / ATP binding
Similarity search - Function
KfrB domain / KfrB protein / Zeta toxin domain / Zeta toxin / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Chem-EPZ / CITRATE ANION / Epsilon_1 antitoxin / Zeta_1 toxin
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsRocker, A. / Meinhart, A.
CitationJournal: Nat Commun / Year: 2018
Title: The ng_ zeta 1 toxin of the gonococcal epsilon/zeta toxin/antitoxin system drains precursors for cell wall synthesis.
Authors: Rocker, A. / Peschke, M. / Kittila, T. / Sakson, R. / Brieke, C. / Meinhart, A.
History
DepositionOct 11, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1May 9, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Epsilon_1 antitoxin
B: Zeta_1 toxin
C: Epsilon_1 antitoxin
D: Zeta_1 toxin
E: Epsilon_1 antitoxin
F: Zeta_1 toxin
G: Epsilon_1 antitoxin
H: Zeta_1 toxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)211,95226
Polymers207,7048
Non-polymers4,24918
Water1,874104
1
A: Epsilon_1 antitoxin
B: Zeta_1 toxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9907
Polymers51,9262
Non-polymers1,0645
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Epsilon_1 antitoxin
D: Zeta_1 toxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9876
Polymers51,9262
Non-polymers1,0614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Epsilon_1 antitoxin
F: Zeta_1 toxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9876
Polymers51,9262
Non-polymers1,0614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Epsilon_1 antitoxin
H: Zeta_1 toxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9907
Polymers51,9262
Non-polymers1,0645
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.290, 148.180, 124.400
Angle α, β, γ (deg.)90.00, 93.88, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
31E
41G
12B
22D
32F
42H

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A1 - 60
2115C1 - 60
3115E1 - 60
4115G1 - 60
1125B1 - 401
2125D1 - 401
3125F1 - 401
4125H1 - 401

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.999064, -0.041903, 0.010756), (0.042109, -0.998918, 0.019736), (0.009917, 0.020171, 0.999747)44.243629, 116.463921, -1.73288
3given(0.998485, -0.054433, 0.008071), (-0.054168, -0.998077, -0.030128), (0.009695, 0.029646, -0.999513)9.88863, 130.787537, 59.16011
4given(-0.99977, -0.002083, 0.021349), (-0.002975, 0.999119, -0.041854), (-0.021243, -0.041908, -0.998896)34.960079, -7.68869, 63.531219
5given(1), (1), (1)
6given(-0.999566, -0.023548, 0.017718), (0.02378, -0.999633, 0.012991), (0.017406, 0.013407, 0.999759)42.377701, 116.875557, -0.99669
7given(0.999629, -0.023494, -0.013794), (-0.023918, -0.99922, -0.031428), (-0.013045, 0.031746, -0.999411)7.68128, 130.227081, 59.555641
8given(-0.99987, -0.010316, 0.012376), (-0.010666, 0.999536, -0.028525), (-0.012076, -0.028654, -0.999516)35.688938, -8.34454, 63.223671

-
Components

-
Protein , 2 types, 8 molecules ACEGBDFH

#1: Protein
Epsilon_1 antitoxin


Mass: 7190.395 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: D5K9E3
#2: Protein
Zeta_1 toxin


Mass: 44735.484 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: D5K9G7

-
Non-polymers , 4 types, 122 molecules

#3: Chemical
ChemComp-EPZ / (2R)-2-{[(2R,3R,4R,5S,6R)-3-(acetylamino)-2-{[(S)-{[(R)-{[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}-5-hydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-4-yl]oxy}propanoic acid


Mass: 679.416 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H31N3O19P2
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 3.55 Å3/Da / Density % sol: 65.4 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / Details: 100 mM sodium citrate pH 4.5, 1.8 M (NH4)2SO4

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 75069 / % possible obs: 99.4 % / Redundancy: 4.2 % / CC1/2: 0.998 / Rrim(I) all: 0.215 / Net I/σ(I): 12
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 1.7 / CC1/2: 0.704 / Rrim(I) all: 0.991 / % possible all: 99.2

-
Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XSCALEdata scaling
Cootmodel building
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EPG

6epg


Resolution: 2.7→49 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.944 / SU B: 14.275 / SU ML: 0.274 / Cross valid method: THROUGHOUT / ESU R: 0.55 / ESU R Free: 0.296 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24545 4064 5.1 %RANDOM
Rwork0.21979 ---
obs0.2212 75069 99.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 66.123 Å2
Baniso -1Baniso -2Baniso -3
1--1.06 Å2-0 Å20.05 Å2
2---4.24 Å2-0 Å2
3---5.24 Å2
Refinement stepCycle: 1 / Resolution: 2.7→49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14039 0 262 104 14405
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01914467
X-RAY DIFFRACTIONr_bond_other_d0.0010.0213554
X-RAY DIFFRACTIONr_angle_refined_deg1.141.96419446
X-RAY DIFFRACTIONr_angle_other_deg0.8292.98631557
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.16251779
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.78124.878695
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.768152758
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.74715100
X-RAY DIFFRACTIONr_chiral_restr0.0880.22137
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0215909
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022779
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.236.5657140
X-RAY DIFFRACTIONr_mcbond_other2.236.5657139
X-RAY DIFFRACTIONr_mcangle_it3.8129.8468911
X-RAY DIFFRACTIONr_mcangle_other3.8129.8468912
X-RAY DIFFRACTIONr_scbond_it2.2736.947327
X-RAY DIFFRACTIONr_scbond_other2.2716.9397325
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.00510.25210535
X-RAY DIFFRACTIONr_long_range_B_refined6.35775.35215147
X-RAY DIFFRACTIONr_long_range_B_other6.35675.35915147
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A309MEDIUM POSITIONAL0.130.5
12C309MEDIUM POSITIONAL0.160.5
13E309MEDIUM POSITIONAL0.140.5
14G309MEDIUM POSITIONAL0.130.5
11A548LOOSE POSITIONAL0.465
12C548LOOSE POSITIONAL0.435
13E548LOOSE POSITIONAL0.535
14G548LOOSE POSITIONAL0.495
11A309MEDIUM THERMAL5.532
12C309MEDIUM THERMAL6.972
13E309MEDIUM THERMAL10.252
14G309MEDIUM THERMAL5.652
11A548LOOSE THERMAL5.9510
12C548LOOSE THERMAL8.1110
13E548LOOSE THERMAL11.5210
14G548LOOSE THERMAL6.510
21B2331MEDIUM POSITIONAL0.210.5
22D2331MEDIUM POSITIONAL0.160.5
23F2331MEDIUM POSITIONAL0.20.5
24H2331MEDIUM POSITIONAL0.190.5
21B3671LOOSE POSITIONAL0.45
22D3671LOOSE POSITIONAL0.355
23F3671LOOSE POSITIONAL0.355
24H3671LOOSE POSITIONAL0.45
21B2331MEDIUM THERMAL5.692
22D2331MEDIUM THERMAL5.642
23F2331MEDIUM THERMAL5.962
24H2331MEDIUM THERMAL5.952
21B3671LOOSE THERMAL5.8310
22D3671LOOSE THERMAL5.710
23F3671LOOSE THERMAL610
24H3671LOOSE THERMAL5.8210
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.401 292 -
Rwork0.386 5489 -
obs--97.83 %

+
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://pdbjlvh1.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