[English] 日本語
Yorodumi
- PDB-3deu: Crystal structure of transcription regulatory protein slyA from S... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3deu
TitleCrystal structure of transcription regulatory protein slyA from Salmonella typhimurium in complex with salicylate ligands
ComponentsTranscriptional regulator slyA
KeywordsTRANSCRIPTION REGULATOR / SlyA / MarR / salmonella / wing-helix / Activator / DNA-binding / Repressor / Transcription regulation / Virulence
Function / homology
Function and homology information


response to stress / DNA-binding transcription factor activity / regulation of DNA-templated transcription / DNA binding / cytoplasm
Similarity search - Function
Transcriptional regulator, SlyA / Transcriptional regulator MarR-type, conserved site / MarR-type HTH domain signature. / : / MarR family / MarR-type HTH domain profile. / helix_turn_helix multiple antibiotic resistance protein / MarR-type HTH domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A ...Transcriptional regulator, SlyA / Transcriptional regulator MarR-type, conserved site / MarR-type HTH domain signature. / : / MarR family / MarR-type HTH domain profile. / helix_turn_helix multiple antibiotic resistance protein / MarR-type HTH domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
2-HYDROXYBENZOIC ACID / Transcriptional regulator SlyA
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLe Trong, I. / Brzovic, P.S. / Fang, F.C. / Libby, S.J. / Stenkamp, R.E.
CitationJournal: Mbio / Year: 2019
Title: The Evolution of SlyA/RovA Transcription Factors from Repressors to Countersilencers in Enterobacteriaceae .
Authors: Will, W.R. / Brzovic, P. / Le Trong, I. / Stenkamp, R.E. / Lawrenz, M.B. / Karlinsey, J.E. / Navarre, W.W. / Main-Hester, K. / Miller, V.L. / Libby, S.J. / Fang, F.C.
History
DepositionJun 10, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Jun 23, 2021Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / struct_ref_seq_dif / struct_site
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 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 slyA
B: Transcriptional regulator slyA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1018
Polymers38,2722
Non-polymers8296
Water34219
1
A: Transcriptional regulator slyA
hetero molecules

A: Transcriptional regulator slyA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1018
Polymers38,2722
Non-polymers8296
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area4860 Å2
ΔGint-35.8 kcal/mol
Surface area14220 Å2
MethodPISA
2
B: Transcriptional regulator slyA
hetero molecules

B: Transcriptional regulator slyA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1018
Polymers38,2722
Non-polymers8296
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area5160 Å2
ΔGint-35.5 kcal/mol
Surface area13820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.382, 78.019, 84.385
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein Transcriptional regulator slyA / Salmolysin / Cytolysin slyA


Mass: 19136.023 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: SGSG 2262 / Gene: slyA, STM1444 / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P40676
#2: Chemical
ChemComp-SAL / 2-HYDROXYBENZOIC ACID / SALICYLIC ACID


Mass: 138.121 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C7H6O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 2.73 Å3/Da / Density % sol: 54.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 20% PEG 300, 10% Glycerol, 0.1 M Phosphate/citrate buffer pH 4.2, 0.2 M Ammonium sulfate, 50 mM Sodium salicylate, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.3776 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 3, 2007 / Details: Adjustable focusing mirrors in K-B geometry
RadiationMonochromator: Si(111) Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3776 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 27988 / Num. obs: 27988 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.9 % / Biso Wilson estimate: 51.8 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 31.7
Reflection shellResolution: 2→2.07 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 1.1 / Num. unique all: 2583 / % possible all: 90.8

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2FBH

2fbh


Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.932 / SU B: 7.186 / SU ML: 0.178 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.264 / ESU R Free: 0.214 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.259 928 5 %RANDOM
Rwork0.228 ---
all0.229 18739 --
obs0.229 18739 97.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 64.71 Å2
Baniso -1Baniso -2Baniso -3
1-4.27 Å20 Å20 Å2
2--0.01 Å20 Å2
3----4.28 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2110 0 60 19 2189
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222198
X-RAY DIFFRACTIONr_bond_other_d00.021516
X-RAY DIFFRACTIONr_angle_refined_deg1.9862.0252964
X-RAY DIFFRACTIONr_angle_other_deg1.0133735
X-RAY DIFFRACTIONr_dihedral_angle_1_deg12.6395258
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.86524.72591
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.715441
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.6391516
X-RAY DIFFRACTIONr_chiral_restr0.1160.2351
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212318
X-RAY DIFFRACTIONr_gen_planes_other00.02378
X-RAY DIFFRACTIONr_mcbond_it2.5231.51309
X-RAY DIFFRACTIONr_mcbond_other0.831.5518
X-RAY DIFFRACTIONr_mcangle_it4.35422129
X-RAY DIFFRACTIONr_scbond_it6.663889
X-RAY DIFFRACTIONr_scangle_it9.8694.5835
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 58 -
Rwork0.267 1275 -
all-1333 -
obs--97.23 %

+
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