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- PDB-8a6x: Crystal structure of a chimeric LOV-Histidine kinase SB2F1 (asymm... -

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Entry
Database: PDB / ID: 8a6x
TitleCrystal structure of a chimeric LOV-Histidine kinase SB2F1 (asymmetrical variant, trigonal form with long c axis)
ComponentsPutative Sensory box protein,Sensor protein FixL
KeywordsSIGNALING PROTEIN / LOV domain / PAS domain / Photocycle / Dimerization / Signaling blue light photoreceptor / sensory histidine kinase / chimeric / De Novo Protein
Function / homology
Function and homology information


histidine phosphotransfer kinase activity / nitrogen fixation / histidine kinase / phosphorelay sensor kinase activity / nucleotide binding / regulation of DNA-templated transcription / ATP binding / metal ion binding
Similarity search - Function
PAS domain / PAS-associated, C-terminal / PAC domain profile. / His Kinase A (phospho-acceptor) domain / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Signal transduction histidine kinase-related protein, C-terminal ...PAS domain / PAS-associated, C-terminal / PAC domain profile. / His Kinase A (phospho-acceptor) domain / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Signal transduction histidine kinase-related protein, C-terminal / 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
ADENOSINE-5'-TRIPHOSPHATE / FLAVIN MONONUCLEOTIDE / Sensor protein FixL / Sensory box protein
Similarity search - Component
Biological speciesPseudomonas putida KT2440 (bacteria)
Bradyrhizobium diazoefficiens USDA 110 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.45 Å
AuthorsArinkin, V. / Granzin, J. / Batra-Safferling, R.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Federal Ministry for Education and ResearchFKZ 031A16 Germany
CitationJournal: To Be Published
Title: Crystal structure of a chimeric LOV-Histidine kinase SB2F1 (asymmetrical variant, trigonal form with long c axis)
Authors: Arinkin, V. / Granzin, J. / Batra-Safferling, R.
History
DepositionJun 20, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 10, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative Sensory box protein,Sensor protein FixL
B: Putative Sensory box protein,Sensor protein FixL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,6656
Polymers86,7382
Non-polymers1,9274
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12770 Å2
ΔGint-79 kcal/mol
Surface area33780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.794, 138.794, 96.084
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 0 through 153 or resid 155 through 363 or resid 402 through 500))
d_2ens_1(chain "B" and (resid 0 through 153 or resid 155 through 363 or resid 402 through 500))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1HISALAA1 - 154
d_12ens_1GLUPROA156 - 364
d_13ens_1ATPATPB
d_14ens_1FMNFMNC
d_21ens_1HISALAD3 - 156
d_22ens_1GLUPROD158 - 366
d_23ens_1ATPATPE
d_24ens_1FMNFMNF

NCS oper: (Code: givenMatrix: (0.997769000525, 5.39269538263E-5, 0.0667609068541), (-0.000896374319881, -0.999898711196, 0.0142043606889), (0.0667549107196, -0.0142325135301, -0.997667889357)Vector: - ...NCS oper: (Code: given
Matrix: (0.997769000525, 5.39269538263E-5, 0.0667609068541), (-0.000896374319881, -0.999898711196, 0.0142043606889), (0.0667549107196, -0.0142325135301, -0.997667889357)
Vector: -1.65793891575, -4.9784628894, 12.024710424)

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Components

#1: Protein Putative Sensory box protein,Sensor protein FixL


Mass: 43368.938 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: De Novo Protein, chimeric, engineered; His-Tag: 1-MGSSHHHHHHSSGLVPRGSH-20; UNP:Q88JB0 (belongs to): 21 (or 1 PDB-file)-(MSE)INA...YYIGIQRDVT-140 (or 120 PDB-file); UNP:P23222 (belongs to): ...Details: De Novo Protein, chimeric, engineered; His-Tag: 1-MGSSHHHHHHSSGLVPRGSH-20; UNP:Q88JB0 (belongs to): 21 (or 1 PDB-file)-(MSE)INA...YYIGIQRDVT-140 (or 120 PDB-file); UNP:P23222 (belongs to):141 (or 121 PDB-file)-EHQQTQ...AADEN-388 (or 368 PDB-file); UNP:Q88JB0 (UNP-numbering) 1-(MSE)INA...QRDVT-120; UNP:P23222 (UNP-numbering) 258 to C-Term; All Met are exchanged for SeMet. Expression system: because of SeMet: E.coli B834 (DE3).
Source: (gene. exp.) Pseudomonas putida KT2440 (bacteria), (gene. exp.) Bradyrhizobium diazoefficiens USDA 110 (bacteria)
Strain: ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440, JCM 10833 / BCRC 13528 / IAM 13628 / NBRC 14792 / USDA 110
Gene: PP_2739, fixL, bll2760 / Production host: Escherichia coli (E. coli) / Strain (production host): B834
References: UniProt: Q88JB0, UniProt: P23222, histidine kinase
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
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: 3.12 Å3/Da / Density % sol: 60.63 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 10% PEG8K, 0.1M Citrate, 0.2M NaCl, 0.1M Ammonium Trifluoroacetate, 1mM ATP, 2mM MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97916 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97916 Å / Relative weight: 1
ReflectionResolution: 2.45→45.43 Å / Num. obs: 27082 / % possible obs: 68.7 % / Redundancy: 20.1 % / Biso Wilson estimate: 77.7 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.028 / Rrim(I) all: 0.125 / Net I/σ(I): 20.2
Reflection shellResolution: 2.452→2.6 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1369 / CC1/2: 0.58 / Rpim(I) all: 0.543 / % possible all: 21.9

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHENIX1.19rc6_4061refinement
XDSdata reduction
Aimlessdata scaling
SHELXDphasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.45→45.43 Å / SU ML: 0.4148 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 36.6228
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Details: The refinement was performed against F(+) and F(-). The number "Unique reflections" given above refers to the "NON-ANOMALOUS" reflections (27081 reflections). However, separating the ...Details: The refinement was performed against F(+) and F(-). The number "Unique reflections" given above refers to the "NON-ANOMALOUS" reflections (27081 reflections). However, separating the reflections on F(+) and F(-), the Phenix program gives a number of 52123 reflections for the refinement. The statistics (number of reflections) in resolution shells also refers to F(+) and F(-). Attention, these are very strong anisotropic data, so that the spherical completeness is relatively low.
RfactorNum. reflection% reflection
Rfree0.2667 1385 5.12 %
Rwork0.2259 49455 -
obs0.2279 27081 68.66 %
Solvent computationShrinkage radii: 1.1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 99.96 Å2
Refinement stepCycle: LAST / Resolution: 2.45→45.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5680 0 124 0 5804
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00785903
X-RAY DIFFRACTIONf_angle_d1.17188007
X-RAY DIFFRACTIONf_chiral_restr0.0636894
X-RAY DIFFRACTIONf_plane_restr0.00581060
X-RAY DIFFRACTIONf_dihedral_angle_d15.6512259
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 2.55550295225 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.540.6683860.62941161X-RAY DIFFRACTION16.47
2.54-2.640.52531520.48812381X-RAY DIFFRACTION33.33
2.64-2.760.43051640.36413062X-RAY DIFFRACTION42.51
2.76-2.910.362520.33193912X-RAY DIFFRACTION55.05
2.91-3.090.33882440.32244857X-RAY DIFFRACTION67.1
3.09-3.330.32372920.30985664X-RAY DIFFRACTION78.88
3.33-3.660.29254240.25346693X-RAY DIFFRACTION93.68
3.66-4.190.2733480.21917245X-RAY DIFFRACTION100
4.19-5.280.20643230.1827266X-RAY DIFFRACTION100
5.28-45.430.23363830.19167214X-RAY DIFFRACTION99.86
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.13020882324-1.21191673757-0.4481682572254.874185285772.686756315853.894077947180.1652602921480.01442347397550.653494377406-0.383053449050.46396040088-0.404681880208-0.5872013636470.855613954088-0.5132044578470.326501969832-0.1937018732630.1654667182860.460951274221-0.1120167511330.37229425301330.2945774447.8225628959711.840084178
29.22998367493-1.23692852748-1.26660165615-0.9552019736760.4135169854610.295746836627-0.094280849807-0.6152049482420.366082598615-0.0248615682376-0.403306553670.424548974214-0.000150809346064-0.950986828790.4419930751630.402685311148-0.01887034985980.007553819264781.44484289149-0.2305772778971.1385711216884.7446279156-4.5306172954814.0202499072
33.594679341131.294138837011.075657571081.17703539119-0.0508978501691.604959883490.418326578503-1.67038053461-0.5315598497010.365601934549-0.4686431174440.6151911342250.447815358572-1.25756746510.06134357904170.705621818674-0.2139287791010.1977657115741.85477390119-0.07420379774451.4444317991977.1473356701-15.324616563215.4729298247
42.006501818211.99858189604-1.134133260642.000620590783.940350469445.39277937349-0.306153767263-0.771192526792-0.9927211196930.3962643731470.1401406076372.321470607160.501072512732-1.381040927430.07792284001530.742931657286-0.4483949514140.07093857105941.92690916249-0.305273309181.3278836183676.0411790396-18.4259564086.79507861695
52.83185319709-2.104050446623.411025817552.08422656392-2.624285638184.147235802370.760534210809-0.7589399599331.84203530330.723952062785-0.543004755962-0.296158182875-0.4347522899090.665675416909-0.04586345149010.565964396639-0.3181581492860.2627027414680.844629836715-0.3008045629340.7764291741134.437185779213.314474255112.0602976062
63.400742787940.2671362181241.782937983945.733016375012.498567384637.160260599480.343010550880.249728091652-0.696530375066-0.2618757325480.23031714243-0.4430388711430.3211740444921.50012587731-0.4518759086130.1960741332310.02184900017660.08289037447910.611489236959-0.1290877589420.4565734419729.2381752979-10.91672129072.07810374434
79.179756463342.203367381141.19815930194-0.8822525887370.3940476027961.064400752180.0867773550490.02653040924690.5453115189010.226648402814-0.5075801297920.3474541829530.17045066572-0.9453494997940.3464127797270.431121219622-0.1113975548520.1518391176771.32070450609-0.1530203125181.4109407435784.4071788112-0.3569034444943.71011525648
84.8983228127-1.193309193490.01341883165791.019401706380.1780329045941.689968492790.2373537074551.442079912910.402877098688-0.248920632985-0.6092487166430.413593676493-0.230627642466-1.034654096680.340466532610.5715785724040.0193588535597-0.02960230636581.4252691404-0.1381795047460.86255417926179.87962309082.521314689870.576572746023
98.373144240860.735729439652.789001289978.5055401389-2.493762901335.83467016124-1.025532693030.08907250821591.73206887919-0.3656523132160.621921357298-0.854411461824-1.119027776360.2191675769450.3602949343870.963601851413-0.0164036445928-0.03940492935951.19697444371-0.230776317491.5615484879172.001023229616.87111143813.47483357215
107.78833597049-9.93805627405-0.5027735255581.9998078988-1.317737743982.00963380180.2786787532491.195420401830.6591149112880.04871539983921.655229654281.17172518466-0.0517804193394-1.42639864743-1.716414186040.8477486127790.440363678564-0.3172079579341.70823749974-0.3540506162891.5481626222974.063758383712.147913387610.9378599025
116.59658516465-3.571846483872.430832526724.68249984785-1.715449754074.85720220156-0.0852618301683-0.0653524474972-1.08190663903-0.6014588512310.745841746235-1.434317242270.7165718938891.31076512015-0.288249878250.4115153974790.2108702730390.08893266193031.20907800238-0.3032369228690.68757896405532.8422363961-16.99561846291.97112865934
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 0 through 119 )AA0 - 1191 - 120
22chain 'A' and (resid 120 through 175 )AA120 - 175121 - 176
33chain 'A' and (resid 176 through 363 )AA176 - 363177 - 364
44chain 'A' and (resid 401 through 401 )AB401
55chain 'A' and (resid 402 through 402 )AC402
66chain 'B' and (resid -2 through 119 )BD-2 - 1191 - 122
77chain 'B' and (resid 120 through 175 )BD120 - 175123 - 178
88chain 'B' and (resid 176 through 274 )BD176 - 274179 - 277
99chain 'B' and (resid 275 through 365 )BD275 - 365278 - 368
1010chain 'B' and (resid 401 through 401 )BE401
1111chain 'B' and (resid 402 through 402 )BF402

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