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- PDB-8js5: Dimeric PAS domains of oxygen sensor FixL with ferric unliganded heme -

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Basic information

Entry
Database: PDB / ID: 8js5
TitleDimeric PAS domains of oxygen sensor FixL with ferric unliganded 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 / Histidine kinase/HSP90-like ATPase superfamily
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Sensor protein FixL
Similarity search - Component
Biological speciesBradyrhizobium diazoefficiens USDA 110 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.95 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)314,09935
Polymers306,55210
Non-polymers7,54625
Water66737
1
A: Sensor protein FixL
B: Sensor protein FixL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,8207
Polymers61,3102
Non-polymers1,5095
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7920 Å2
ΔGint-83 kcal/mol
Surface area26770 Å2
MethodPISA
2
C: Sensor protein FixL
D: Sensor protein FixL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,8207
Polymers61,3102
Non-polymers1,5095
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7670 Å2
ΔGint-82 kcal/mol
Surface area26520 Å2
MethodPISA
3
E: Sensor protein FixL
F: Sensor protein FixL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,8207
Polymers61,3102
Non-polymers1,5095
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7270 Å2
ΔGint-81 kcal/mol
Surface area27030 Å2
MethodPISA
4
G: Sensor protein FixL
H: Sensor protein FixL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,8207
Polymers61,3102
Non-polymers1,5095
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7370 Å2
ΔGint-80 kcal/mol
Surface area26630 Å2
MethodPISA
5
I: Sensor protein FixL
J: Sensor protein FixL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,8207
Polymers61,3102
Non-polymers1,5095
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7470 Å2
ΔGint-78 kcal/mol
Surface area26750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)190.443, 194.147, 269.857
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 / Feature type: SUBJECT OF INVESTIGATION
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 4.07 Å3/Da / Density % sol: 69.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 1.5 M ammonium sulfate, 0.1 M TrisHCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 31, 2019 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.95→47.88 Å / Num. obs: 104696 / % possible obs: 99.8 % / Redundancy: 8.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.04 / Rrim(I) all: 0.113 / Net I/σ(I): 15.8 / Num. measured all: 843998 / Scaling rejects: 33
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
2.95-38.21.924113850000.4660.7072.0481.197.7
16.16-47.885.80.024385666810.010.02647.593.6

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Processing

Software
NameVersionClassification
PHENIX1.20.1refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
XDS20180409data reduction
SHELX2018/2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.95→28.65 Å / SU ML: 0.3636 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.5771
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2463 5298 5.07 %
Rwork0.2068 99179 -
obs0.2088 104477 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 149.22 Å2
Refinement stepCycle: LAST / Resolution: 2.95→28.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19756 0 520 37 20313
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005520767
X-RAY DIFFRACTIONf_angle_d1.010428202
X-RAY DIFFRACTIONf_chiral_restr0.05092976
X-RAY DIFFRACTIONf_plane_restr0.00733670
X-RAY DIFFRACTIONf_dihedral_angle_d15.65617607
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.95-2.980.38611760.36213152X-RAY DIFFRACTION97.25
2.98-3.020.35731700.32343348X-RAY DIFFRACTION100
3.02-3.060.31551700.29793219X-RAY DIFFRACTION99.88
3.06-3.090.31411870.29313306X-RAY DIFFRACTION99.86
3.09-3.140.36761860.28293255X-RAY DIFFRACTION99.91
3.14-3.180.3011890.28043292X-RAY DIFFRACTION99.89
3.18-3.220.31621700.26983270X-RAY DIFFRACTION99.94
3.22-3.270.29531630.27183277X-RAY DIFFRACTION99.97
3.27-3.320.29991980.23993284X-RAY DIFFRACTION99.86
3.32-3.380.26371590.25313293X-RAY DIFFRACTION99.97
3.38-3.440.27881740.24153305X-RAY DIFFRACTION99.97
3.44-3.50.30571710.24923287X-RAY DIFFRACTION99.97
3.5-3.560.30781800.233289X-RAY DIFFRACTION100
3.57-3.640.25141770.20813293X-RAY DIFFRACTION100
3.64-3.720.24071890.19593277X-RAY DIFFRACTION100
3.72-3.80.22751720.19513305X-RAY DIFFRACTION99.94
3.8-3.90.24791760.19283296X-RAY DIFFRACTION99.97
3.9-40.19611940.17283311X-RAY DIFFRACTION99.97
4-4.120.19611640.17943321X-RAY DIFFRACTION99.97
4.12-4.250.1821840.16313308X-RAY DIFFRACTION99.97
4.25-4.40.22841610.16663309X-RAY DIFFRACTION100
4.4-4.580.17571550.15673327X-RAY DIFFRACTION100
4.58-4.790.20341660.15943323X-RAY DIFFRACTION100
4.79-5.040.21321830.16593354X-RAY DIFFRACTION100
5.04-5.350.23681890.21253264X-RAY DIFFRACTION100
5.35-5.760.29981700.22213359X-RAY DIFFRACTION100
5.76-6.340.30391790.25093340X-RAY DIFFRACTION100
6.34-7.240.26381910.21163366X-RAY DIFFRACTION99.97
7.24-9.070.20481750.19833414X-RAY DIFFRACTION100
9.07-28.650.24861800.20453435X-RAY DIFFRACTION98.31

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