[English] 日本語
Yorodumi
- PDB-44ms: VcFadRqm, a quadruple mutant (Y153A, K156E, L203F, L208F) of fatt... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 44ms
TitleVcFadRqm, a quadruple mutant (Y153A, K156E, L203F, L208F) of fatty acid metabolism regulator protein from Vibrio cholerae, in complex with oleoyl-CoA
ComponentsFatty acid metabolism regulator protein
KeywordsTRANSCRIPTION / DNA BINDING PROTEIN
Function / homology
Function and homology information


fatty-acyl-CoA binding / regulation of 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 DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Chem-3VV / : / Fatty acid metabolism regulator protein
Similarity search - Component
Biological speciesVibrio cholerae O395 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.58 Å
AuthorsTsui, W. / Ma, J.B.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: VcFadRqm, a quadruple mutant (Y153A, K156E, L203F, L208F) of fatty acid metabolism regulator protein from Vibrio cholerae, in complex with oleoyl-CoA
Authors: Tsui, W. / Ma, J.B.
History
DepositionAug 4, 2026Deposition site: PDBJ / Processing site: PDBC
SupersessionSep 16, 2026ID: 8Y41
Revision 1.0Sep 16, 2026Provider: repository / Type: Initial release

-
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)66,5358
Polymers64,0212
Non-polymers2,5146
Water1,42379
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.726, 57.335, 57.483
Angle α, β, γ (deg.)67.921, 63.352, 90.023
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
d_1ens_1(chain "A" and ((resid 10 through 15 and (name N...
d_2ens_1(chain "B" and (resid 10 through 33 or (resid 34...
d_1ens_2chain "C"
d_2ens_2chain "D"

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_1ens_1GLYGLYPROPROAA10 - 27110 - 271
d_2ens_1GLYGLYPROPROBB10 - 27110 - 271
d_1ens_23VV3VV3VV3VVAC301
d_2ens_23VV3VV3VV3VVBF301

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(0.99994147528961, 0.010810521034934, 0.00042264712525304), (0.01080941884352, -0.99993837968606, 0.0025284966037183), (0.00044995544732576, -0.0025237800543869, -0.99999671403177)-0.19058785310723, -0.10157063213641, -0.03915031391966
2given(0.99110349335909, 0.079956940249578, -0.10639902799054), (0.076902634580568, -0.99650836781355, -0.032512423350914), (-0.10862711561104, 0.024040810791377, -0.99379182385977)-1.8462600212608, -1.1527478853363, 1.0268344922031

-
Components

#1: Protein Fatty acid metabolism regulator protein


Mass: 32010.541 Da / Num. of mol.: 2 / Mutation: Y153A, K156E, L203F, L208F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O395 (bacteria) / Gene: fadR, VC0395_A1490, VC395_2015
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A5F6Z2
#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.: 2 / Source method: obtained synthetically / Formula: C39H68N7O17P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cd
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 43.03 %
Crystal growTemperature: 300 K / Method: in cell
Details: 0.05M Cadmium sulfate hydrate, 0.1M Hepes,1M sodium acetate trihydrate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 17, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.579→20 Å / Num. obs: 16083 / % possible obs: 96.6909 % / Redundancy: 3 % / Biso Wilson estimate: 35.81 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 20.699
Reflection shellResolution: 2.579→2.78 Å / Num. unique obs: 15530 / CC1/2: 0.02

-
Processing

Software
NameVersionClassification
PHENIX2.0_5936refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.58→19.49 Å / SU ML: 0.3113 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 32.5256
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2761 716 4.45 %
Rwork0.2567 15367 -
obs0.2577 16083 95.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.54 Å2
Refinement stepCycle: LAST / Resolution: 2.58→19.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3921 0 138 79 4138
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044148
X-RAY DIFFRACTIONf_angle_d0.82855639
X-RAY DIFFRACTIONf_chiral_restr0.0441607
X-RAY DIFFRACTIONf_plane_restr0.0079728
X-RAY DIFFRACTIONf_dihedral_angle_d23.74631475
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS1.9218079863947
ens_2d_2CAX-RAY DIFFRACTIONTorsion NCS4.0007624111305
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.58-2.780.30351360.28022700X-RAY DIFFRACTION85.78
2.78-3.060.35991290.28123171X-RAY DIFFRACTION96.83
3.06-3.50.26181540.26263131X-RAY DIFFRACTION98.27
3.5-4.40.25511400.24693184X-RAY DIFFRACTION98.49
4.4-19.490.26691570.24623181X-RAY DIFFRACTION98.79
Refinement TLS params.Method: refined / Origin x: 0.45116977185056 Å / Origin y: 0.01219433183914 Å / Origin z: 0.11569857799306 Å
111213212223313233
T0.31393720810948 Å20.012023099421965 Å2-0.026106501291957 Å2-0.18350217162064 Å2-0.018156281854366 Å2--0.19177444315837 Å2
L0.4595142347976 °20.045887532872102 °20.059167658954566 °2-1.0498846462384 °2-0.20106069279919 °2--0.69669490022813 °2
S-0.012374539105724 Å °-0.011058707292979 Å °0.0081445033049002 Å °-0.042548183452181 Å °0.0065460538698581 Å °0.058429825093022 Å °0.0053462042427638 Å °0.0065433048487367 Å °0.01331972193203 Å °
Refinement TLS groupSelection details: all

+
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