[English] 日本語
Yorodumi
- PDB-5ydv: Regulatory domain of HypT from Salmonella typhimurium complexed w... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ydv
TitleRegulatory domain of HypT from Salmonella typhimurium complexed with HOCl (HOCl-bound form)
ComponentsCell density-dependent motility repressor
KeywordsDNA BINDING PROTEIN / HypT / HOCl / HOCl-specific transcription factor / LysR-type transcription regulator / Hypochlorous acid / hypochlorite / regulatory domain
Function / homology
Function and homology information


amino acid biosynthetic process / transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / DNA binding
Similarity search - Function
LysR, substrate-binding / LysR substrate binding domain / LysR-type HTH domain profile. / Transcription regulator HTH, LysR / Bacterial regulatory helix-turn-helix protein, lysR family / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
hypochlorous acid / Cell density-dependent motility repressor / LysR family transcriptional regulator
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.752 Å
AuthorsJo, I. / Hong, S. / Ahn, J. / Ha, N.C.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2019
Title: Structural basis for HOCl recognition and regulation mechanisms of HypT, a hypochlorite-specific transcriptional regulator.
Authors: Jo, I. / Kim, D. / No, T. / Hong, S. / Ahn, J. / Ryu, S. / Ha, N.C.
History
DepositionSep 14, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 28, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cell density-dependent motility repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0363
Polymers23,8871
Non-polymers1492
Water3,207178
1
A: Cell density-dependent motility repressor
hetero molecules

A: Cell density-dependent motility repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0726
Polymers47,7752
Non-polymers2974
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area2530 Å2
ΔGint-48 kcal/mol
Surface area19160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.293, 63.293, 101.438
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-560-

HOH

-
Components

#1: Protein Cell density-dependent motility repressor / Quorum-sensing regulator protein D


Mass: 23887.254 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: HOCl (or hypochlorite ion) sulfate ion / Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: qseD_2, DD95_15310, STMU2UK_04484 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0J5DK07, UniProt: Q7CP75*PLUS
#2: Chemical ChemComp-8TR / hypochlorous acid


Mass: 52.460 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: ClHO
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 2.13 Å3/Da / Density % sol: 42.16 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M lithium sulfate, 0.1M sodium cacodylate (pH 6.5), and 30%(v/v) PEG 400

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.75→20 Å / Num. obs: 21030 / % possible obs: 98.1 % / Redundancy: 18.4 % / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.012 / Net I/σ(I): 42.61
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.325 / Mean I/σ(I) obs: 4.98 / Num. unique obs: 1032 / Rpim(I) all: 0.112 / % possible all: 99.4

-
Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
DENZOdata reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YDO

5ydo


Resolution: 1.752→19.48 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.56 / Phase error: 23.26
RfactorNum. reflection% reflection
Rfree0.2532 1017 4.94 %
Rwork0.2087 --
obs0.2109 20597 96.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.752→19.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1679 0 7 178 1864
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051727
X-RAY DIFFRACTIONf_angle_d0.7742342
X-RAY DIFFRACTIONf_dihedral_angle_d2.8721443
X-RAY DIFFRACTIONf_chiral_restr0.051258
X-RAY DIFFRACTIONf_plane_restr0.004306
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.752-1.84430.28711390.25242447X-RAY DIFFRACTION87
1.8443-1.95970.2811400.23052835X-RAY DIFFRACTION99
1.9597-2.11090.28431440.22022857X-RAY DIFFRACTION100
2.1109-2.3230.26331460.2122862X-RAY DIFFRACTION100
2.323-2.65840.2321330.21252926X-RAY DIFFRACTION100
2.6584-3.34660.26231720.20452902X-RAY DIFFRACTION100
3.3466-19.48080.23051430.19192751X-RAY DIFFRACTION89
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.71710.01750.78472.16270.18222.37210.16740.079-0.0765-0.3164-0.04460.04840.05760.05490.04240.06940.0475-0.04450.16720.04660.170240.292315.300337.8984
22.05390.1425-0.04251.50780.30011.99090.0310.0831-0.1148-0.2518-0.0146-0.06650.2094-0.2687-0.0420.03930.02310.02470.1608-0.02610.106126.417514.194519.964
33.03670.2626-1.46012.1156-0.83913.7487-0.0789-0.0606-0.2365-0.0653-0.1208-0.0378-0.0109-0.23980.10640.13260.06730.03660.14050.03730.090328.505317.939414.9905
41.28840.79581.29750.53171.19325.07850.2847-0.3113-0.21370.2289-0.2438-0.14380.5703-0.20560.05950.1375-0.065-0.0250.21530.09460.183732.312610.061542.004
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 95 through 154 )
2X-RAY DIFFRACTION2chain 'A' and (resid 155 through 194 )
3X-RAY DIFFRACTION3chain 'A' and (resid 195 through 270 )
4X-RAY DIFFRACTION4chain 'A' and (resid 271 through 302 )

+
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