[English] 日本語
Yorodumi
- PDB-9ncx: NitrOFF1 "ON" State -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9ncx
TitleNitrOFF1 "ON" State
ComponentsEngineered fluorescent biosensor NitrOFF1 "ON" State
KeywordsFLUORESCENT PROTEIN / Nitrate / Recombinant
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsSmailys, J. / Zhang, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM128923 United States
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2025
Title: NitrOFF: An Engineered Fluorescent Biosensor to Illuminate Nitrate Transport in Living Cells.
Authors: Cook, M.A. / Smailys, J.D. / Ji, K. / Phelps, S.M. / Tutol, J.N. / Kim, W. / Ong, W.S.Y. / Peng, W. / Maydew, C. / Zhang, Y.J. / Dodani, S.C.
History
DepositionFeb 17, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 17, 2025Provider: repository / Type: Initial release
Revision 1.1Oct 8, 2025Group: Database references / Category: citation / Item: _citation.journal_volume

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Engineered fluorescent biosensor NitrOFF1 "ON" State
B: Engineered fluorescent biosensor NitrOFF1 "ON" State
C: Engineered fluorescent biosensor NitrOFF1 "ON" State
D: Engineered fluorescent biosensor NitrOFF1 "ON" State


Theoretical massNumber of molelcules
Total (without water)173,7084
Polymers173,7084
Non-polymers00
Water00
1
A: Engineered fluorescent biosensor NitrOFF1 "ON" State


Theoretical massNumber of molelcules
Total (without water)43,4271
Polymers43,4271
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Engineered fluorescent biosensor NitrOFF1 "ON" State


Theoretical massNumber of molelcules
Total (without water)43,4271
Polymers43,4271
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Engineered fluorescent biosensor NitrOFF1 "ON" State


Theoretical massNumber of molelcules
Total (without water)43,4271
Polymers43,4271
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Engineered fluorescent biosensor NitrOFF1 "ON" State


Theoretical massNumber of molelcules
Total (without water)43,4271
Polymers43,4271
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)132.905, 188.352, 188.280
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein
Engineered fluorescent biosensor NitrOFF1 "ON" State


Mass: 43427.020 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.58 Å3/Da / Density % sol: 65.68 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 1M Ammonium Phosphate, 0.1M TRIS pH (7.0)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.999 Å
DetectorType: DECTRIS EIGER2 X CdTe 16M / Detector: PIXEL / Date: Jan 24, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 2.89→56.77 Å / Num. obs: 48832 / % possible obs: 93.23 % / Redundancy: 4 % / CC1/2: 0.977 / Rmerge(I) obs: 0.222 / Rpim(I) all: 0.125 / Net I/σ(I): 7.2
Reflection shellResolution: 2.89→3.05 Å / Rmerge(I) obs: 0.879 / Num. unique obs: 2195 / CC1/2: 0.374

-
Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
xia2data scaling
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→56.77 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2798 1998 4.51 %
Rwork0.238 --
obs0.2399 44262 93.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→56.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11584 0 0 0 11584
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00511820
X-RAY DIFFRACTIONf_angle_d1.09315988
X-RAY DIFFRACTIONf_dihedral_angle_d17.4911632
X-RAY DIFFRACTIONf_chiral_restr0.0641760
X-RAY DIFFRACTIONf_plane_restr0.0062080
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.080.37641440.31463010X-RAY DIFFRACTION94
3.08-3.160.32171440.29113068X-RAY DIFFRACTION96
3.16-3.250.3541440.28723049X-RAY DIFFRACTION95
3.25-3.360.38661450.28513055X-RAY DIFFRACTION95
3.36-3.480.30791440.26933047X-RAY DIFFRACTION95
3.48-3.620.27911450.25973067X-RAY DIFFRACTION95
3.62-3.780.30131430.24773024X-RAY DIFFRACTION95
3.78-3.980.29681430.24863048X-RAY DIFFRACTION94
3.98-4.230.29311410.2332985X-RAY DIFFRACTION93
4.23-4.560.22331430.19563019X-RAY DIFFRACTION93
4.56-5.010.23691430.20083037X-RAY DIFFRACTION92
5.01-5.740.2561390.21142947X-RAY DIFFRACTION91
5.74-7.230.25091410.23582970X-RAY DIFFRACTION90
7.23-56.770.24831390.21292938X-RAY DIFFRACTION86

+
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