[English] 日本語
Yorodumi
- PDB-5ztj: Crystal Structure of GyraseA C-Terminal Domain from Salmonella ty... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ztj
TitleCrystal Structure of GyraseA C-Terminal Domain from Salmonella typhi at 2.4A Resolution
ComponentsDNA gyrase subunit A
KeywordsDNA BINDING PROTEIN / Topoisomerase / Gyr-CTD / beta propeller
Function / homology
Function and homology information


DNA negative supercoiling activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / DNA-templated DNA replication / chromosome / DNA binding / ATP binding / cytoplasm
Similarity search - Function
DNA gyrase/topoisomerase IV, subunit A, C-terminal / DNA gyrase, subunit A / DNA gyrase/topoisomerase IV, subunit A, C-terminal repeat / DNA gyrase/topoisomerase IV, subunit A, C-terminal / : / DNA gyrase C-terminal domain, beta-propeller / DNA topoisomerase, type IIA, alpha-helical domain superfamily / DNA topoisomerase, type IIA, domain A / DNA topoisomerase, type IIA, domain A, alpha-beta / DNA gyrase/topoisomerase IV, subunit A ...DNA gyrase/topoisomerase IV, subunit A, C-terminal / DNA gyrase, subunit A / DNA gyrase/topoisomerase IV, subunit A, C-terminal repeat / DNA gyrase/topoisomerase IV, subunit A, C-terminal / : / DNA gyrase C-terminal domain, beta-propeller / DNA topoisomerase, type IIA, alpha-helical domain superfamily / DNA topoisomerase, type IIA, domain A / DNA topoisomerase, type IIA, domain A, alpha-beta / DNA gyrase/topoisomerase IV, subunit A / DNA Topoisomerase IV / DNA topoisomerase, type IIA-like domain superfamily / 6 Propeller / Neuraminidase / Mainly Beta
Similarity search - Domain/homology
DNA gyrase subunit A
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSachdeva, E. / Gupta, D. / Tiwari, P. / Kaur, G. / Sharma, S. / Singh, T.P. / Ethayathulla, A.S. / Kaur, P.
CitationJournal: Sci Rep / Year: 2020
Title: The pivot point arginines identified in the beta-pinwheel structure of C-terminal domain from Salmonella Typhi DNA Gyrase A subunit.
Authors: Sachdeva, E. / Kaur, G. / Tiwari, P. / Gupta, D. / Singh, T.P. / Ethayathulla, A.S. / Kaur, P.
History
DepositionMay 3, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 1.1May 27, 2020Group: 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
Revision 1.2Nov 22, 2023Group: 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
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA gyrase subunit A


Theoretical massNumber of molelcules
Total (without water)33,8871
Polymers33,8871
Non-polymers00
Water1,964109
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13830 Å2
Unit cell
Length a, b, c (Å)79.150, 79.150, 87.357
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein DNA gyrase subunit A


Mass: 33886.559 Da / Num. of mol.: 1 / Fragment: UNP residues 531-840
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhi (bacteria)
Gene: gyrA / Plasmid: pET-28(a) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: A0A1U7FVV6, EC: 5.99.1.3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.02 Å3/Da / Density % sol: 39.07 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, Magnesium Chloride hexahydrate, glycerol

-
Data collection

DiffractionMean temperature: 273 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9919 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 31, 2017
RadiationMonochromator: double-crystal fixed-exit Bragg monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9919 Å / Relative weight: 1
ReflectionResolution: 2.4→58.66 Å / Num. obs: 20743 / % possible obs: 99.9 % / Redundancy: 5.6 % / Biso Wilson estimate: 48.4 Å2 / CC1/2: 0.998 / Rsym value: 0.076 / Net I/σ(I): 14.89
Reflection shellResolution: 2.4→2.64 Å / Mean I/σ(I) obs: 2.87 / Num. unique obs: 3331 / CC1/2: 0.874 / Rsym value: 0.583 / % possible all: 99.5

-
Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZI0

1zi0


Resolution: 2.4→47.125 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.51 / Stereochemistry target values: ML
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.2418 590 5.22 %
Rwork0.1901 --
obs0.1927 11308 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→47.125 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2197 0 0 109 2306
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032220
X-RAY DIFFRACTIONf_angle_d0.6393006
X-RAY DIFFRACTIONf_dihedral_angle_d11.3881354
X-RAY DIFFRACTIONf_chiral_restr0.047363
X-RAY DIFFRACTIONf_plane_restr0.003391
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4001-2.64170.30351460.21182619X-RAY DIFFRACTION100
2.6417-3.02390.3071550.22022632X-RAY DIFFRACTION100
3.0239-3.80950.26081430.18842631X-RAY DIFFRACTION98
3.8095-47.13440.20351460.17952836X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 26.4383 Å / Origin y: 22.912 Å / Origin z: 22.2724 Å
111213212223313233
T0.2485 Å2-0.017 Å20.0246 Å2-0.2893 Å20.0178 Å2--0.2816 Å2
L2.0223 °2-0.9479 °20.2532 °2-1.2108 °2-0.0688 °2--0.9539 °2
S0.138 Å °0.1473 Å °0.1432 Å °-0.113 Å °-0.1662 Å °-0.0373 Å °-0.0748 Å °0.0077 Å °-0.0003 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