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- PDB-10jx: Crystal structure of heme binding PAS domain from one component t... -

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Basic information

Entry
Database: PDB / ID: 10jx
TitleCrystal structure of heme binding PAS domain from one component transcription factor, FG214
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 / IMIDAZOLE / 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: 1.47 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)34,56716
Polymers32,4952
Non-polymers2,07314
Water3,297183
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7840 Å2
ΔGint-75 kcal/mol
Surface area16230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.346, 64.932, 105.973
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

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Components

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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

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Non-polymers , 10 types, 197 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-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cl
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#9: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#10: Chemical ChemComp-POL / N-PROPANOL / 1-PROPONOL


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

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

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.920194 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 20, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.920194 Å / Relative weight: 1
ReflectionResolution: 1.467→34.451 Å / Num. obs: 75338 / % possible obs: 99.9 % / Redundancy: 7.7 % / Biso Wilson estimate: 18.76 Å2 / CC1/2: 0.992 / Net I/σ(I): 9.8
Reflection shellResolution: 1.467→1.493 Å / Num. unique obs: 3680 / CC1/2: 0.355

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
AutoSolphasing
autoPROCdata processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.47→34.45 Å / SU ML: 0.1461 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.6729
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1901 3708 4.92 %
Rwork0.1641 71593 -
obs0.1654 75301 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.07 Å2
Refinement stepCycle: LAST / Resolution: 1.47→34.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2218 0 139 184 2541
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00632533
X-RAY DIFFRACTIONf_angle_d0.86773468
X-RAY DIFFRACTIONf_chiral_restr0.0787369
X-RAY DIFFRACTIONf_plane_restr0.007455
X-RAY DIFFRACTIONf_dihedral_angle_d19.3201968
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.47-1.490.29851320.30442691X-RAY DIFFRACTION99.37
1.49-1.510.30011450.27812692X-RAY DIFFRACTION99.51
1.51-1.530.28451680.25362684X-RAY DIFFRACTION99.82
1.53-1.550.24541270.23692747X-RAY DIFFRACTION99.97
1.55-1.580.23921260.22012730X-RAY DIFFRACTION100
1.58-1.60.23641540.19742719X-RAY DIFFRACTION100
1.6-1.630.23031410.19842745X-RAY DIFFRACTION99.97
1.63-1.660.21841480.18142736X-RAY DIFFRACTION100
1.66-1.690.21450.16432693X-RAY DIFFRACTION100
1.69-1.730.19741480.15452717X-RAY DIFFRACTION100
1.73-1.760.18971510.15132748X-RAY DIFFRACTION100
1.76-1.80.19711470.14622716X-RAY DIFFRACTION99.97
1.8-1.850.16981630.13632723X-RAY DIFFRACTION99.86
1.85-1.90.20811400.14462742X-RAY DIFFRACTION99.93
1.9-1.950.1951390.13672725X-RAY DIFFRACTION100
1.95-2.020.15731410.13562757X-RAY DIFFRACTION99.93
2.02-2.090.15921120.13472794X-RAY DIFFRACTION99.97
2.09-2.170.15471510.14192744X-RAY DIFFRACTION99.97
2.17-2.270.18061140.14182770X-RAY DIFFRACTION99.97
2.27-2.390.16791680.1442759X-RAY DIFFRACTION100
2.39-2.540.20471250.15512791X-RAY DIFFRACTION100
2.54-2.740.17621460.16352780X-RAY DIFFRACTION100
2.74-3.010.18671590.17452773X-RAY DIFFRACTION100
3.01-3.450.23061400.17452813X-RAY DIFFRACTION100
3.45-4.340.17021380.1562843X-RAY DIFFRACTION99.4
4.34-34.450.17681400.17042961X-RAY DIFFRACTION99.33

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