[English] 日本語
Yorodumi
- PDB-1h9g: FadR, FATTY ACID RESPONSIVE TRANSCRIPTION FACTOR FROM E. COLI, in... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1h9g
TitleFadR, FATTY ACID RESPONSIVE TRANSCRIPTION FACTOR FROM E. COLI, in complex with myristoyl-CoA
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 / fatty acid metabolic process / DNA-binding transcription factor activity / negative 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 / GntR-type HTH domain profile. / helix_turn_helix gluconate operon transcriptional repressor / Transcription regulator HTH, GntR / Bacterial regulatory proteins, gntR family / 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 / GntR-type HTH domain profile. / helix_turn_helix gluconate operon transcriptional repressor / Transcription regulator HTH, GntR / Bacterial regulatory proteins, gntR family / 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
COENZYME A / MYRISTIC ACID / Fatty acid metabolism regulator protein / Fatty acid metabolism regulator protein
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsVan Aalten, D.M.F. / Dirusso, C.C. / Knudsen, J.
Citation
Journal: Embo J. / Year: 2001
Title: The Structural Basis of Acyl Coenzyme A-Dependent Regulation of the Transcription Factor Fadr
Authors: Van Aalten, D.M.F. / Dirusso, C.C. / Knudsen, J.
#1: 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. / Dirusso, C.C. / Knudsen, J. / Wierenga, R.K.
#2: 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
DepositionMar 9, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 9, 2001Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_database_status / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag

-
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)28,4893
Polymers27,4931
Non-polymers9962
Water2,414134
1
A: FATTY ACID METABOLISM REGULATOR PROTEIN
hetero molecules

A: FATTY ACID METABOLISM REGULATOR PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,9786
Polymers54,9862
Non-polymers1,9924
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
MethodPQS
Unit cell
Length a, b, c (Å)59.476, 59.476, 290.483
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-2123-

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-COA / COENZYME A / Coenzyme A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical ChemComp-MYR / MYRISTIC ACID / Myristic acid


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 2.7 Å3/Da / Density % sol: 54.4 %
Crystal growpH: 7 / Details: pH 7.00
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
14.6 mg/mlprotein1drop
250 mM1dropKH2PO4
310 %glycerol1drop
5200 mMmagnesium acetate1reservoir
6100 mMsodium cacodylate1reservoir
4myristoyl-CoA1drop2-fold molar excess

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.93
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 2, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 18556 / % possible obs: 97.8 % / Redundancy: 4.7 % / Biso Wilson estimate: 31.9 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 17.9
Reflection shellResolution: 2.1→2.18 Å / Rmerge(I) obs: 0.292 / Mean I/σ(I) obs: 5 / % possible all: 95.5
Reflection shell
*PLUS
% possible obs: 95.5 %

-
Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1E2X

1e2x


Resolution: 2.1→29.68 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 2029989.25 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: SOME RESIDUES TRUNCATED TO ALA O DUE TO POORLY DEFINED ELECTRON DENSITY
RfactorNum. reflection% reflectionSelection details
Rfree0.256 595 3.2 %RANDOM
Rwork0.226 ---
obs0.226 18450 97.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 82 Å2 / ksol: 0.431178 e/Å3
Displacement parametersBiso mean: 43.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å2-1.79 Å20 Å2
2--0.28 Å20 Å2
3----0.57 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2.1→29.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1781 0 63 134 1978
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
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_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.14
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.71.5
X-RAY DIFFRACTIONc_mcangle_it2.582
X-RAY DIFFRACTIONc_scbond_it2.52
X-RAY DIFFRACTIONc_scangle_it3.742.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.307 91 3.2 %
Rwork0.269 2786 -
obs--94.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ADEPYR.PAR&_1_TOPOLOGY_INFILE_3
X-RAY DIFFRACTION4PANMYR.PAR&_1_TOPOLOGY_INFILE_4
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_deg20
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.14

+
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