[English] 日本語
Yorodumi
- PDB-10jy: Crystal structure of heme binding PAS domain from one component t... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 10jy
TitleCrystal structure of heme binding PAS domain from one component transcription factor, FG214 reduced with dithionite
ComponentsMulti-sensor signal transduction histidine kinase
KeywordsTRANSCRIPTION / transcription factor / heme / PAS domain / bacterial signaling
Function / homology
Function and homology information


kinase activity / regulation of DNA-templated transcription / DNA binding
Similarity search - Function
LuxR-type HTH domain profile. / Transcription regulator LuxR, C-terminal / Bacterial regulatory proteins, luxR family / helix_turn_helix, Lux Regulon / Signal transduction response regulator, C-terminal effector / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain ...LuxR-type HTH domain profile. / Transcription regulator LuxR, C-terminal / Bacterial regulatory proteins, luxR family / helix_turn_helix, Lux Regulon / Signal transduction response regulator, C-terminal effector / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
FORMIC ACID / PROTOPORPHYRIN IX CONTAINING FE / PHOSPHATE ION / N-PROPANOL / Multi-sensor signal transduction histidine kinase
Similarity search - Component
Biological speciesFimbriimonas ginsengisoli Gsoil 348 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsSiclari, J.J. / Isiorho, E.A. / Gardner, K.H.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM106239 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM156296 United States
CitationJournal: To Be Published
Title: Crystal structure of heme binding PAS domain from one component transcription factor, FG214
Authors: Siclari, J.J. / Isiorho, E.A. / Gardner, K.H.
History
DepositionJan 22, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Multi-sensor signal transduction histidine kinase
B: Multi-sensor signal transduction histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0359
Polymers32,4952
Non-polymers1,5407
Water3,099172
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6820 Å2
ΔGint-67 kcal/mol
Surface area15440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.030, 65.210, 105.870
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Multi-sensor signal transduction histidine kinase


Mass: 16247.333 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fimbriimonas ginsengisoli Gsoil 348 (bacteria)
Gene: OP10G_3234 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A068NTE8

-
Non-polymers , 5 types, 179 molecules

#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-POL / N-PROPANOL / 1-PROPONOL


Mass: 60.095 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C3H8O
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.35 Å3/Da / Density % sol: 63.26 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.2M Sodium formate, 0.2M Ammonium acetate, 0.2M Sodium citrate tribasic dihydrate, 0.2M Potassium sodium tartrate tetrahydrate, 0.2M Sodium oxamate, 0.2M 1,6-Hexanediol, 0.2M 1-Butanol 0.2M ...Details: 0.2M Sodium formate, 0.2M Ammonium acetate, 0.2M Sodium citrate tribasic dihydrate, 0.2M Potassium sodium tartrate tetrahydrate, 0.2M Sodium oxamate, 0.2M 1,6-Hexanediol, 0.2M 1-Butanol 0.2M 1,2-Propanediol, 0.2M 2-Propanol, 0.2M 1,4-Butanediol, 0.2M 1,3-Propanediol, 0.4M Imidazole, 0.6M MES monohydrate, 25% v/v MPD, 25% PEG 1000, 25% w/v PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 30, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.648→55.523 Å / Num. obs: 393593 / % possible obs: 100 % / Redundancy: 7.4 % / Biso Wilson estimate: 31.32 Å2 / CC1/2: 0.999 / Net I/σ(I): 11
Reflection shellResolution: 1.648→1.677 Å / Num. unique obs: 20404 / CC1/2: 0.382

-
Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
autoPROCdata processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→45.32 Å / SU ML: 0.2372 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.3373
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2154 2635 4.95 %
Rwork0.1876 50627 -
obs0.1889 53262 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.67 Å2
Refinement stepCycle: LAST / Resolution: 1.65→45.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2246 0 105 172 2523
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01062446
X-RAY DIFFRACTIONf_angle_d1.11723348
X-RAY DIFFRACTIONf_chiral_restr0.057359
X-RAY DIFFRACTIONf_plane_restr0.0169439
X-RAY DIFFRACTIONf_dihedral_angle_d17.0081914
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.680.37661420.38242575X-RAY DIFFRACTION97.52
1.68-1.710.41151430.36822616X-RAY DIFFRACTION99.14
1.71-1.750.31471210.33472617X-RAY DIFFRACTION99.67
1.75-1.780.32171090.29772656X-RAY DIFFRACTION99.89
1.78-1.830.29561160.26512660X-RAY DIFFRACTION100
1.83-1.870.28761400.26912629X-RAY DIFFRACTION99.89
1.87-1.920.27131520.26382631X-RAY DIFFRACTION99.96
1.92-1.980.24651580.2412625X-RAY DIFFRACTION99.96
1.98-2.040.2351490.2082637X-RAY DIFFRACTION99.96
2.04-2.110.22561560.19172633X-RAY DIFFRACTION99.89
2.11-2.20.20891570.18042622X-RAY DIFFRACTION99.96
2.2-2.30.20811250.18792666X-RAY DIFFRACTION100
2.3-2.420.21911340.18662687X-RAY DIFFRACTION99.96
2.42-2.570.25961320.19462665X-RAY DIFFRACTION100
2.57-2.770.22871520.1872672X-RAY DIFFRACTION100
2.77-3.050.1941340.19152689X-RAY DIFFRACTION100
3.05-3.490.21981550.19182707X-RAY DIFFRACTION99.93
3.49-4.40.1841150.14922762X-RAY DIFFRACTION99.97
4.4-45.320.17491450.15642878X-RAY DIFFRACTION99.9

+
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