[English] 日本語
Yorodumi
- PDB-36bz: Crystal structure of QUI1 complexed with quinine -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 36bz
TitleCrystal structure of QUI1 complexed with quinine
ComponentsQUI1
KeywordsTRANSCRIPTION / Transcription repressor / Biosensor / Monoterpene Indole Alkaloid (MIA) binding protein / RamR
Function / homologyQuinine / :
Function and homology information
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsHong, Y. / Zhang, Y.J.
Funding support United States, Denmark, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM148356 United States
Novo Nordisk FoundationNNF22SA0078231 Denmark
Novo Nordisk FoundationNNF20CC0035580 Denmark
CitationJournal: Biorxiv / Year: 2026
Title: Engineering Biosensors to Enhance Monoterpene Indole Alkaloid Production in Yeast.
Authors: Holtz, M. / d'Oelsnitz, S. / Domingo, C.C. / Madsen, N.G. / Hong, M.Y. / Arnesen, J.A. / van Aalst, A.C.A. / de Haan, S. / Weingarten, C.K. / Welner, D.H. / Silver, P.A. / Zhang, Y.J. / ...Authors: Holtz, M. / d'Oelsnitz, S. / Domingo, C.C. / Madsen, N.G. / Hong, M.Y. / Arnesen, J.A. / van Aalst, A.C.A. / de Haan, S. / Weingarten, C.K. / Welner, D.H. / Silver, P.A. / Zhang, Y.J. / Jensen, M.K. / Acevedo-Rocha, C.G.
History
DepositionMay 29, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: QUI1
B: QUI1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5254
Polymers43,8762
Non-polymers6492
Water4,288238
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2440 Å2
ΔGint-16 kcal/mol
Surface area16650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.739, 39.733, 105.618
Angle α, β, γ (deg.)90.000, 113.133, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

-
Components

#1: Protein QUI1


Mass: 21938.018 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: A0A0D6H745
#2: Chemical ChemComp-QI9 / Quinine / (3alpha,8alpha,9R)-6'-methoxycinchonan-9-ol


Mass: 324.417 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C20H24N2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / 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: 2.08 Å3/Da / Density % sol: 40.96 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 6mg/mL protein in 200mM NaCl, 8% PEG6000, 30mM MES pH 6.0, 60mM potassium iodide

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.968 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jul 18, 2025
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.968 Å / Relative weight: 1
ReflectionResolution: 1.77→48.56 Å / Num. obs: 35307 / % possible obs: 99.08 % / Redundancy: 4.2 % / Biso Wilson estimate: 23.4 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.076 / Rrim(I) all: 0.155 / Net I/σ(I): 11.9
Reflection shellResolution: 1.77→1.8 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.879 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1710 / CC1/2: 0.619 / Rpim(I) all: 0.472 / Rrim(I) all: 1.001 / % possible all: 98.79

-
Processing

Software
NameVersionClassification
PHENIX2.0.5761refinement
xia2data reduction
xia2data scaling
PHENIX2.0.5761phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.77→48.56 Å / SU ML: 0.246 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.2353
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2705 2008 5.7 %
Rwork0.224 33204 -
obs0.2266 35212 98.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.62 Å2
Refinement stepCycle: LAST / Resolution: 1.77→48.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2898 0 48 238 3184
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00663006
X-RAY DIFFRACTIONf_angle_d0.80394062
X-RAY DIFFRACTIONf_chiral_restr0.0436450
X-RAY DIFFRACTIONf_plane_restr0.0077516
X-RAY DIFFRACTIONf_dihedral_angle_d17.56641102
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.77-1.810.33221430.27612327X-RAY DIFFRACTION98.29
1.81-1.860.33611530.26672312X-RAY DIFFRACTION99
1.86-1.920.33551290.25362384X-RAY DIFFRACTION99.25
1.92-1.980.29461530.24752368X-RAY DIFFRACTION99.41
1.98-2.050.31641400.2392377X-RAY DIFFRACTION99.41
2.05-2.130.26881430.22212353X-RAY DIFFRACTION99.32
2.13-2.230.29321430.22992390X-RAY DIFFRACTION99.18
2.23-2.350.29521380.22512359X-RAY DIFFRACTION98.73
2.35-2.50.27611370.23562279X-RAY DIFFRACTION95.31
2.5-2.690.25981430.23282395X-RAY DIFFRACTION99.72
2.69-2.960.24371430.22662392X-RAY DIFFRACTION99.76
2.96-3.390.2741490.22072405X-RAY DIFFRACTION99.53
3.39-4.270.25211410.19322400X-RAY DIFFRACTION98.22
4.27-48.560.24981530.22152463X-RAY DIFFRACTION98.35

+
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