[English] 日本語
Yorodumi
- PDB-1e2x: FadR, fatty acid responsive transcription factor from E. coli -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1e2x
TitleFadR, fatty acid responsive transcription factor from E. coli
ComponentsFATTY ACID METABOLISM REGULATOR PROTEIN
KeywordsTRANSCRIPTIONAL REGULATION
Function / homology
Function and homology information


fatty-acyl-CoA binding / regulation of fatty acid metabolic process / positive regulation of fatty acid biosynthetic process / cis-regulatory region sequence-specific DNA binding / fatty acid metabolic process / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / protein homodimerization activity ...fatty-acyl-CoA binding / regulation of fatty acid metabolic process / positive regulation of fatty acid biosynthetic process / cis-regulatory region sequence-specific DNA binding / fatty acid metabolic process / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / protein homodimerization activity / DNA binding / cytosol
Similarity search - Function
Fatty acid response transcription factor FadR / FadR, C-terminal domain / FadR C-terminal domain / GntR ligand-binding domain-like / Transcription regulator FadR/GntR, C-terminal / Transcription regulator HTH, GntR / Bacterial regulatory proteins, gntR family / GntR-type HTH domain profile. / helix_turn_helix gluconate operon transcriptional repressor / Four Helix Bundle (Hemerythrin (Met), subunit A) ...Fatty acid response transcription factor FadR / FadR, C-terminal domain / FadR C-terminal domain / GntR ligand-binding domain-like / Transcription regulator FadR/GntR, C-terminal / Transcription regulator HTH, GntR / Bacterial regulatory proteins, gntR family / GntR-type HTH domain profile. / helix_turn_helix gluconate operon transcriptional repressor / Four Helix Bundle (Hemerythrin (Met), subunit A) / 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 / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Fatty acid metabolism regulator protein / Fatty acid metabolism regulator protein
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsVan Aalten, D.M.F. / Dirusso, C.C. / Knudsen, J. / Wierenga, R.K.
Citation
Journal: Embo J. / Year: 2000
Title: Crystal Structure of Fadr, a Fatty Acid-Responsive Transcription Factor with a Novel Acyl Coenzyme A-Binding Fold
Authors: Van Aalten, D.M.F. / Dirusso, C.C. / Knudsen, J. / Wierenga, R.K.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Crystallization and X-Ray Diffraction Studies of the Fatty-Acid Responsive Transcription Factor Fadr from Escherichia Coli.
Authors: Van Aalten, D.M.F. / Knudsen, J. / Dirusso, C.C. / Kokko, T. / Wierenga, R.K.
History
DepositionMay 30, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 3, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: FATTY ACID METABOLISM REGULATOR PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6853
Polymers27,4931
Non-polymers1922
Water2,810156
1
A: FATTY ACID METABOLISM REGULATOR PROTEIN
hetero molecules

A: FATTY ACID METABOLISM REGULATOR PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3706
Polymers54,9862
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
MethodPQS
Unit cell
Length a, b, c (Å)59.711, 101.973, 87.513
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-4002-

SO4

21A-2045-

HOH

-
Components

#1: Protein FATTY ACID METABOLISM REGULATOR PROTEIN


Mass: 27493.111 Da / Num. of mol.: 1 / Fragment: FULL LENGTH
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P09371, UniProt: P0A8V6*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 2.48 Å3/Da / Density % sol: 50.05 %
Crystal growpH: 9 / Details: LI2SO4/(NH4)2SO4, TRIS PH 9
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
14.6 mg/mlprotein1drop
250 mM1dropKH2PO4
310 %glycerol1drop
42.3 Mammonium sulfate1reservoir
50.75 M1reservoirLiSO4
6100 mMTris-HCl1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9535, 1.0
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 15, 2000
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.95351
211
ReflectionResolution: 2→25 Å / Num. obs: 18125 / % possible obs: 95.2 % / Redundancy: 3.2 % / Biso Wilson estimate: 16.9 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 9.7
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.448 / Mean I/σ(I) obs: 2.6 / % possible all: 74
Reflection shell
*PLUS
% possible obs: 73.8 %

-
Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNS1phasing
RefinementMethod to determine structure: MAD / Resolution: 2→24.48 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1880425.42 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: SOME RESIDUES TRUNCATED TO ALA OR GLY DUE TO POORLY DEFINED ELECTRON DENSITY
RfactorNum. reflection% reflectionSelection details
Rfree0.237 744 4.1 %RANDOM
Rwork0.2 ---
obs0.2 17945 97.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.9511 Å2 / ksol: 0.35566 e/Å3
Displacement parametersBiso mean: 27.8 Å2
Baniso -1Baniso -2Baniso -3
1-5.27 Å20 Å20 Å2
2---8.58 Å20 Å2
3---3.31 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2→24.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1746 0 10 156 1912
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.351.5
X-RAY DIFFRACTIONc_mcangle_it2.052
X-RAY DIFFRACTIONc_scbond_it2.222
X-RAY DIFFRACTIONc_scangle_it3.312.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.329 110 3.9 %
Rwork0.27 2741 -
obs--94.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1

+
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