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- PDB-8js6: Dimeric PAS domains of oxygen sensor FixL in complex with cyanide... -

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Basic information

Entry
Database: PDB / ID: 8js6
TitleDimeric PAS domains of oxygen sensor FixL in complex with cyanide-bound ferric heme
ComponentsSensor protein FixL
KeywordsTRANSFERASE / heme-binding / PAS / coiled-coil
Function / homology
Function and homology information


histidine phosphotransfer kinase activity / nitrogen fixation / phosphorelay sensor kinase activity / histidine kinase / 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
CYANIDE ION / PROTOPORPHYRIN IX CONTAINING FE / Sensor protein FixL
Similarity search - Component
Biological speciesBradyrhizobium diazoefficiens USDA 110 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / SAD / Resolution: 2.7 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)314,35945
Polymers306,55210
Non-polymers7,80635
Water1,13563
1
A: Sensor protein FixL
B: Sensor protein FixL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,8729
Polymers61,3102
Non-polymers1,5617
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8280 Å2
ΔGint-77 kcal/mol
Surface area26310 Å2
MethodPISA
2
C: Sensor protein FixL
D: Sensor protein FixL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,8729
Polymers61,3102
Non-polymers1,5617
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8020 Å2
ΔGint-79 kcal/mol
Surface area26320 Å2
MethodPISA
3
E: Sensor protein FixL
F: Sensor protein FixL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,8729
Polymers61,3102
Non-polymers1,5617
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7630 Å2
ΔGint-75 kcal/mol
Surface area27070 Å2
MethodPISA
4
G: Sensor protein FixL
H: Sensor protein FixL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,8729
Polymers61,3102
Non-polymers1,5617
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7410 Å2
ΔGint-77 kcal/mol
Surface area26530 Å2
MethodPISA
5
I: Sensor protein FixL
J: Sensor protein FixL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,8729
Polymers61,3102
Non-polymers1,5617
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7750 Å2
ΔGint-77 kcal/mol
Surface area26620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)187.834, 198.733, 266.320
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
Source: (gene. exp.) Bradyrhizobium diazoefficiens USDA 110 (bacteria)
Gene: fixL, bll2760 / Plasmid: pE-SUMO Amp / 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-CYN / CYANIDE ION


Mass: 26.017 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: CN / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 4.05 Å3/Da / Density % sol: 69.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 1.5 M Ammonium sulfate, 0.1 M MES, 0.05 M KCN

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1.7382 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7382 Å / Relative weight: 1
ReflectionResolution: 2.7→49.69 Å / Num. obs: 135992 / % possible obs: 100 % / Redundancy: 13.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.03 / Rrim(I) all: 0.109 / Net I/σ(I): 15.5 / Num. measured all: 1799377 / Scaling rejects: 1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.7-2.7514.22.4019551167070.5820.6592.491.2100
14.79-49.6912.60.037114779080.9990.0110.03950.497.6

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
PHENIX1.20.1refinement
Aimless0.7.3data scaling
SHELX2018/2phasing
PDB_EXTRACT3.27data extraction
XDS20180126data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→49.68 Å / SU ML: 0.3887 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.364
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 + omega-cdl
RfactorNum. reflection% reflection
Rfree0.2472 6822 5.02 %
Rwork0.2186 129092 -
obs0.22 135914 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 135.19 Å2
Refinement stepCycle: LAST / Resolution: 2.7→49.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19830 0 540 63 20433
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007320849
X-RAY DIFFRACTIONf_angle_d1.0728283
X-RAY DIFFRACTIONf_chiral_restr0.05742982
X-RAY DIFFRACTIONf_plane_restr0.00953686
X-RAY DIFFRACTIONf_dihedral_angle_d28.61957624
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.730.38941890.37944303X-RAY DIFFRACTION99.67
2.73-2.760.35292440.34934241X-RAY DIFFRACTION100
2.76-2.80.3332100.32244321X-RAY DIFFRACTION99.98
2.8-2.830.33522430.30454218X-RAY DIFFRACTION99.98
2.83-2.870.24752030.28214276X-RAY DIFFRACTION99.96
2.87-2.910.30382030.28294316X-RAY DIFFRACTION99.96
2.91-2.950.31922330.28624233X-RAY DIFFRACTION100
2.95-2.990.30182140.28224305X-RAY DIFFRACTION99.93
2.99-3.040.27852380.2784278X-RAY DIFFRACTION100
3.04-3.090.34842380.32454238X-RAY DIFFRACTION99.93
3.09-3.140.33792310.34554254X-RAY DIFFRACTION99.96
3.14-3.20.32422460.30994273X-RAY DIFFRACTION100
3.2-3.260.29032350.27874295X-RAY DIFFRACTION99.96
3.26-3.330.26372220.24194285X-RAY DIFFRACTION99.93
3.33-3.40.23922450.21964259X-RAY DIFFRACTION100
3.4-3.480.23642020.21684319X-RAY DIFFRACTION99.98
3.48-3.570.23362390.22134272X-RAY DIFFRACTION100
3.57-3.660.28992510.23454262X-RAY DIFFRACTION99.98
3.66-3.770.26982180.24414292X-RAY DIFFRACTION99.98
3.77-3.890.25682200.21394316X-RAY DIFFRACTION100
3.89-4.030.21072490.20694287X-RAY DIFFRACTION99.98
4.03-4.190.21062090.19534295X-RAY DIFFRACTION100
4.19-4.380.21142320.18364313X-RAY DIFFRACTION99.98
4.39-4.620.20872090.1794335X-RAY DIFFRACTION99.96
4.62-4.90.20472280.17664336X-RAY DIFFRACTION99.87
4.91-5.280.20922370.19274317X-RAY DIFFRACTION99.91
5.28-5.810.29212320.23524331X-RAY DIFFRACTION99.98
5.81-6.650.25342290.22624389X-RAY DIFFRACTION100
6.65-8.370.23932360.2064387X-RAY DIFFRACTION99.98
8.38-49.680.23032370.17964546X-RAY DIFFRACTION99.69

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