[English] 日本語
Yorodumi
- PDB-4y15: SdiA in complex with 3-oxo-C6-homoserine lactone -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4y15
TitleSdiA in complex with 3-oxo-C6-homoserine lactone
ComponentsTranscriptional regulator of ftsQAZ gene cluster
KeywordsDNA BINDING PROTEIN / Quorum sensor
Function / homology
Function and homology information


regulation of DNA-templated transcription / DNA binding
Similarity search - Function
Transcription factor LuxR-like, autoinducer-binding domain / Transcription factor LuxR-like, autoinducer-binding domain / Transcription factor LuxR-like, autoinducer-binding domain superfamily / Autoinducer binding domain / LuxR-type HTH domain signature. / LuxR-type HTH domain profile. / Transcription regulator LuxR, C-terminal / Bacterial regulatory proteins, luxR family / helix_turn_helix, Lux Regulon / Signal transduction response regulator, C-terminal effector ...Transcription factor LuxR-like, autoinducer-binding domain / Transcription factor LuxR-like, autoinducer-binding domain / Transcription factor LuxR-like, autoinducer-binding domain superfamily / Autoinducer binding domain / LuxR-type HTH domain signature. / LuxR-type HTH domain profile. / Transcription regulator LuxR, C-terminal / Bacterial regulatory proteins, luxR family / helix_turn_helix, Lux Regulon / Signal transduction response regulator, C-terminal effector / Beta-Lactamase / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-482 / Quorum-sensing transcriptional activator
Similarity search - Component
Biological speciesEscherichia coli O157:H7 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.835 Å
AuthorsNguyen, N.X. / Nguyen, Y. / Sperandio, V. / Jiang, Y.
CitationJournal: Mbio / Year: 2015
Title: Structural and Mechanistic Roles of Novel Chemical Ligands on the SdiA Quorum-Sensing Transcription Regulator.
Authors: Nguyen, Y. / Nguyen, N.X. / Rogers, J.L. / Liao, J. / MacMillan, J.B. / Jiang, Y. / Sperandio, V.
History
DepositionFeb 6, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2015Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Sep 27, 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: Transcriptional regulator of ftsQAZ gene cluster
B: Transcriptional regulator of ftsQAZ gene cluster
C: Transcriptional regulator of ftsQAZ gene cluster
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,7638
Polymers86,9323
Non-polymers8325
Water1267
1
A: Transcriptional regulator of ftsQAZ gene cluster
C: Transcriptional regulator of ftsQAZ gene cluster
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,4775
Polymers57,9542
Non-polymers5233
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4950 Å2
ΔGint-28 kcal/mol
Surface area22750 Å2
MethodPISA
2
B: Transcriptional regulator of ftsQAZ gene cluster
hetero molecules

B: Transcriptional regulator of ftsQAZ gene cluster
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5736
Polymers57,9542
Non-polymers6194
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area4850 Å2
ΔGint-41 kcal/mol
Surface area22310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.620, 92.694, 119.698
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein Transcriptional regulator of ftsQAZ gene cluster


Mass: 28977.174 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Strain: O157:H7 / Gene: sdiA, ECs2654, Z3004 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8XBD0
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-482 / 3-oxo-N-[(3S)-2-oxotetrahydrofuran-3-yl]hexanamide


Mass: 213.230 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15NO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.83 Å3/Da / Density % sol: 56.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 18% (w/v) PEG 3350, 0.1M sodium acetate pH5.4, 0.3M ammonium sulfate
PH range: 5.2-5.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.987 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 2, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.835→41.554 Å / Num. obs: 23699 / % possible obs: 98.61 % / Redundancy: 5 % / Rsym value: 0.103 / Net I/σ(I): 20.2
Reflection shellHighest resolution: 2.835 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 1.6 / % possible all: 97.7

-
Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Y13

4y13


Resolution: 2.835→41.554 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2532 1187 5.01 %
Rwork0.2293 --
obs0.2305 23699 98.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.835→41.554 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5844 0 55 7 5906
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046040
X-RAY DIFFRACTIONf_angle_d0.9728178
X-RAY DIFFRACTIONf_dihedral_angle_d14.3232258
X-RAY DIFFRACTIONf_chiral_restr0.041873
X-RAY DIFFRACTIONf_plane_restr0.0041058
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8355-2.96450.35831420.32172601X-RAY DIFFRACTION93
2.9645-3.12070.35151440.29692783X-RAY DIFFRACTION99
3.1207-3.31620.2871470.29362816X-RAY DIFFRACTION100
3.3162-3.57210.3321500.25322810X-RAY DIFFRACTION100
3.5721-3.93130.251500.23372817X-RAY DIFFRACTION100
3.9313-4.49960.22051480.20462839X-RAY DIFFRACTION99
4.4996-5.66670.23431540.20452868X-RAY DIFFRACTION100
5.6667-41.55860.2161520.20362978X-RAY DIFFRACTION98

+
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