[English] 日本語
Yorodumi
- PDB-4pdk: FadR, Fatty Acid Responsive Transcription Factor from Vibrio chol... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4pdk
TitleFadR, Fatty Acid Responsive Transcription Factor from Vibrio cholerae, in Complex with oleoyl-CoA
ComponentsFatty acid metabolism regulator protein
KeywordsTRANSCRIPTION / transcription regulator
Function / homology
Function and homology information


negative regulation of phospholipid biosynthetic process / fatty-acyl-CoA binding / regulation of fatty acid metabolic process / fatty acid metabolic process / DNA-binding transcription factor activity / DNA binding / cytoplasm
Similarity search - Function
Fatty acid response transcription factor FadR / FadR, C-terminal domain / FadR C-terminal domain / 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 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A ...Fatty acid response transcription factor FadR / FadR, C-terminal domain / FadR C-terminal domain / 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 / 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
Chem-3VV / Fatty acid metabolism regulator protein
Similarity search - Component
Biological speciesVibrio cholerae serotype O1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsShi, W. / Kull, F.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI072661 United States
CitationJournal: Nat Commun / Year: 2015
Title: The 40-residue insertion in Vibrio cholerae FadR facilitates binding of an additional fatty acyl-CoA ligand.
Authors: Shi, W. / Kovacikova, G. / Lin, W. / Taylor, R.K. / Skorupski, K. / Kull, F.J.
History
DepositionApr 19, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 18, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Derived calculations
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Derived calculations ...Author supporting evidence / Derived calculations / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_struct_oper_list / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 27, 2023Group: 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
B: Fatty acid metabolism regulator protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,1976
Polymers64,0692
Non-polymers4,1284
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3570 Å2
ΔGint-17 kcal/mol
Surface area26130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.920, 88.690, 62.860
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and segid
21chain B and segid

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and segidA0
211chain B and segidB0

-
Components

#1: Protein Fatty acid metabolism regulator protein


Mass: 32034.670 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae serotype O1 (ATCC 39315 / El Tor Inaba N16961) (bacteria)
Strain: ATCC 39315 / El Tor Inaba N16961 / Gene: fadR, VC_1900 / Plasmid: pTXB1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9KQU8
#2: Chemical
ChemComp-3VV / S-{(3R,5R,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-3,5-dioxido-10,14-dioxo-2,4,6-trioxa-11,15-diaza-3lambda~5~,5lambda~5~-diphosphaheptadecan-17-yl} (9Z)-octadec-9-enethioate (non-preferred name) / oleoyl-CoA


Mass: 1031.980 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C39H68N7O17P3S

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 55.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 17% PEG 3350, 0.23M magnesium formate

-
Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Sep 28, 2013
RadiationMonochromator: SI(111) CHANNEL CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.8→19.73 Å / Num. obs: 16577 / % possible obs: 99.3 % / Redundancy: 3.63 % / Biso Wilson estimate: 35.03 Å2 / Net I/σ(I): 11.48

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata reduction
XSCALEdata scaling
PHASER(phenix.molecular replacement: 1.8.4_1496)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→19.73 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 31.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2982 1654 9.99 %
Rwork0.2585 14904 -
obs0.2628 16558 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 244.3 Å2 / Biso mean: 73.2325 Å2 / Biso min: 2.42 Å2
Refinement stepCycle: final / Resolution: 2.8→19.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4240 0 268 0 4508
Biso mean--59.13 --
Num. residues----524
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014610
X-RAY DIFFRACTIONf_angle_d2.1486236
X-RAY DIFFRACTIONf_chiral_restr0.095656
X-RAY DIFFRACTIONf_plane_restr0.009774
X-RAY DIFFRACTIONf_dihedral_angle_d22.5281724
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2211X-RAY DIFFRACTION14.043TORSIONAL
12B2211X-RAY DIFFRACTION14.043TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8-2.88220.41350.3611226136199
2.8822-2.97490.35041350.31681203133899
2.9749-3.08080.35041340.322712221356100
3.0808-3.20370.39321350.30351213134899
3.2037-3.34880.30351360.28971224136099
3.3488-3.52440.30681370.271212351372100
3.5244-3.74380.30111380.257412351373100
3.7438-4.03060.26571370.250512451382100
4.0306-4.43210.27361380.226312441382100
4.4321-5.0640.29211380.213412481386100
5.064-6.34470.28621440.243412861430100
6.3447-19.730.23641470.21721323147099
Refinement TLS params.Method: refined / Origin x: 16.9316 Å / Origin y: -20.042 Å / Origin z: -9.1424 Å
111213212223313233
T0.0825 Å2-0.0277 Å20.0138 Å2--0.0094 Å20.0526 Å2---0.0459 Å2
L0.0024 °20.0125 °20.0099 °2-0.0093 °2-0.0109 °2--0.0189 °2
S-0.055 Å °-0.0149 Å °-0.0786 Å °-0.0185 Å °-0.0372 Å °0.0702 Å °0.0071 Å °-0.0537 Å °-0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA8 - 266
2X-RAY DIFFRACTION1allA1267 - 1268
3X-RAY DIFFRACTION1allB8 - 1268

+
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