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- PDB-8js7: Dimeric PAS domains of oxygen sensor FixL in complex with imidazo... -

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Basic information

Entry
Database: PDB / ID: 8js7
TitleDimeric PAS domains of oxygen sensor FixL in complex with imidazole-bound heme
ComponentsSensor protein FixL
KeywordsTRANSFERASE / heme-binding / PAS / coiled-coil
Function / homology
Function and homology information


histidine phosphotransfer kinase activity / nitrogen fixation / histidine kinase / phosphorelay sensor kinase activity / phosphorelay signal transduction system / regulation of DNA-templated transcription / ATP binding / metal ion binding / plasma membrane
Similarity search - Function
: / PAS-associated, C-terminal / PAC domain profile. / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / Signal transduction histidine kinase-related protein, C-terminal / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily ...: / PAS-associated, C-terminal / PAC domain profile. / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / Signal transduction histidine kinase-related protein, C-terminal / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Histidine kinase domain / Histidine kinase domain profile. / PAS fold / PAS fold / PAS domain / PAS repeat profile. / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / PAS domain / PAS domain superfamily / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase superfamily
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / IMIDAZOLE / Sensor protein FixL
Similarity search - Component
Biological speciesBradyrhizobium diazoefficiens USDA 110 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsKamaya, M. / Koteishi, H. / Sawai, H. / Sugimoto, H. / Shiro, Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
Citation
Journal: To be published
Title: Dimeric PAS domains of oxygen sensor FixL in complex with imidazole-bound heme.
Authors: Koteishi, H. / Sugimoto, H.
#1: Journal: Sci Signal / Year: 2018
Title: Architecture of the complete oxygen-sensing FixL-FixJ two-component signal transduction system.
Authors: Wright, G.S.A. / Saeki, A. / Hikima, T. / Nishizono, Y. / Hisano, T. / Kamaya, M. / Nukina, K. / Nishitani, H. / Nakamura, H. / Yamamoto, M. / Antonyuk, S.V. / Hasnain, S.S. / Shiro, Y. / Sawai, H.
History
DepositionJun 19, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 26, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sensor protein FixL
B: Sensor protein FixL
C: Sensor protein FixL
D: Sensor protein FixL
E: Sensor protein FixL
F: Sensor protein FixL
G: Sensor protein FixL
H: Sensor protein FixL
I: Sensor protein FixL
J: Sensor protein FixL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)314,78945
Polymers306,55210
Non-polymers8,23735
Water1,27971
1
A: Sensor protein FixL
B: Sensor protein FixL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,9589
Polymers61,3102
Non-polymers1,6477
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8340 Å2
ΔGint-69 kcal/mol
Surface area26690 Å2
MethodPISA
2
C: Sensor protein FixL
D: Sensor protein FixL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,9589
Polymers61,3102
Non-polymers1,6477
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8330 Å2
ΔGint-74 kcal/mol
Surface area26460 Å2
MethodPISA
3
E: Sensor protein FixL
F: Sensor protein FixL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,9589
Polymers61,3102
Non-polymers1,6477
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7780 Å2
ΔGint-67 kcal/mol
Surface area26890 Å2
MethodPISA
4
G: Sensor protein FixL
H: Sensor protein FixL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,9589
Polymers61,3102
Non-polymers1,6477
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8040 Å2
ΔGint-67 kcal/mol
Surface area26890 Å2
MethodPISA
5
I: Sensor protein FixL
J: Sensor protein FixL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,9589
Polymers61,3102
Non-polymers1,6477
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7700 Å2
ΔGint-70 kcal/mol
Surface area26930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)188.854, 199.313, 270.010
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein
Sensor protein FixL


Mass: 30655.225 Da / Num. of mol.: 10 / Fragment: oxygen sensor domain
Source method: isolated from a genetically manipulated source
Details: oxygen sensor domain
Source: (gene. exp.) Bradyrhizobium diazoefficiens USDA 110 (bacteria)
Gene: fixL, bll2760 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P23222, histidine kinase
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H5N2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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

CrystalDensity Matthews: 4.14 Å3/Da / Density % sol: 70.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 1.5 M Ammonium sulfate, 0.1 M Sodium Acetate, 10 mM Imidazole

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 12, 2019
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. obs: 117838 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 7.21 % / Biso Wilson estimate: 73.49 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.16 / Net I/σ(I): 10.5
Reflection shellResolution: 2.85→3.02 Å / Redundancy: 7.25 % / Mean I/σ(I) obs: 1.04 / Num. unique obs: 36309 / CC1/2: 0.493 / Rrim(I) all: 1.69 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDS20180808data scaling
Coot0.9.6model building
PHENIX1.20.1_4487phasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.85→49.83 Å / SU ML: 0.3746 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.7624
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 + omega-cdl
RfactorNum. reflection% reflection
Rfree0.2482 5941 5.04 %
Rwork0.2158 111897 -
obs0.2174 117838 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 115.19 Å2
Refinement stepCycle: LAST / Resolution: 2.85→49.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19789 0 570 71 20430
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005620867
X-RAY DIFFRACTIONf_angle_d1.153428315
X-RAY DIFFRACTIONf_chiral_restr0.0932981
X-RAY DIFFRACTIONf_plane_restr0.00826203
X-RAY DIFFRACTIONf_dihedral_angle_d28.43847619
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-2.880.35671590.31853393X-RAY DIFFRACTION91.64
2.88-2.920.32791980.31813755X-RAY DIFFRACTION99.95
2.92-2.950.31331900.30933652X-RAY DIFFRACTION100
2.95-2.990.32991930.30813745X-RAY DIFFRACTION100
2.99-3.030.2921750.28493717X-RAY DIFFRACTION99.97
3.03-3.070.28992230.27593681X-RAY DIFFRACTION100
3.07-3.120.33322100.28783732X-RAY DIFFRACTION100
3.12-3.160.34531920.31253682X-RAY DIFFRACTION100
3.16-3.210.38982140.34153719X-RAY DIFFRACTION100
3.21-3.260.28142080.2943753X-RAY DIFFRACTION100
3.26-3.320.2971990.26453663X-RAY DIFFRACTION100
3.32-3.380.30241940.25073716X-RAY DIFFRACTION99.97
3.38-3.450.32382100.24443730X-RAY DIFFRACTION99.97
3.45-3.520.27891750.24413727X-RAY DIFFRACTION100
3.52-3.590.29462110.24433708X-RAY DIFFRACTION100
3.59-3.680.26952060.23443705X-RAY DIFFRACTION100
3.68-3.770.25842070.22823724X-RAY DIFFRACTION100
3.77-3.870.27181850.24653747X-RAY DIFFRACTION100
3.87-3.980.25772000.20243728X-RAY DIFFRACTION99.97
3.98-4.110.21282130.19953718X-RAY DIFFRACTION100
4.11-4.260.19471830.18673747X-RAY DIFFRACTION99.97
4.26-4.430.2112030.17553777X-RAY DIFFRACTION99.97
4.43-4.630.20321770.16873726X-RAY DIFFRACTION100
4.63-4.870.19921970.16933783X-RAY DIFFRACTION100
4.87-5.180.19452020.17013742X-RAY DIFFRACTION100
5.18-5.580.22441990.20353783X-RAY DIFFRACTION100
5.58-6.140.25872020.23473771X-RAY DIFFRACTION100
6.14-7.030.24812080.21053799X-RAY DIFFRACTION100
7.03-8.840.23032000.18943832X-RAY DIFFRACTION100
8.84-49.830.21822080.18053942X-RAY DIFFRACTION99.31

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