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- PDB-8a52: Crystal structure of a chimeric LOV-Histidine kinase SB2F1 (asymm... -

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Basic information

Entry
Database: PDB / ID: 8a52
TitleCrystal structure of a chimeric LOV-Histidine kinase SB2F1 (asymmetrical variant, trigonal form with long c-axis)
ComponentsPutative Sensory box protein,Putative 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 / phosphorelay signal transduction system / nucleotide binding / regulation of DNA-templated transcription / ATP binding / metal ion binding / plasma membrane
Similarity search - Function
: / PAS domain / 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 ...: / PAS domain / 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
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: 2.461 Å
AuthorsBatra-Safferling, R. / Arinkin, V. / Granzin, J.
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: Batra-Safferling, R. / Arinkin, V. / Granzin, J. / Krauss, U.
History
DepositionJun 14, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 27, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative Sensory box protein,Putative Sensory box protein,Sensor protein FixL
B: Putative Sensory box protein,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 area12830 Å2
ΔGint-87 kcal/mol
Surface area33280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.246, 138.246, 94.990
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_1chain "A"
d_2ens_1chain "B"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1HISPROA1 - 364
d_12ens_1ATPATPB
d_13ens_1FMNFMNC
d_21ens_1HISPROD1 - 364
d_22ens_1ATPATPE
d_23ens_1FMNFMNF

NCS oper: (Code: givenMatrix: (0.996100160904, -0.00422795977666, 0.0881282803849), (-0.00452557884215, -0.999984710943, 0.00317758018743), (0.0881134983054, -0.00356401961709, -0.996104065437)Vector: ...NCS oper: (Code: given
Matrix: (0.996100160904, -0.00422795977666, 0.0881282803849), (-0.00452557884215, -0.999984710943, 0.00317758018743), (0.0881134983054, -0.00356401961709, -0.996104065437)
Vector: -1.80048917001, -5.37924950109, 10.4755942522)

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Components

#1: Protein Putative Sensory box 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: OTHER_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 ...Details: OTHER_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-MINA...QRDVT-120; UNP:P23222 (UNP-NUMBERING) 258 TO C-TERM; ALL MET ARE EXCHANGED FOR SEMET. EXPRESSIONSYSTEM: 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
Gene: PP_2739 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: Q88JB0, UniProt: P23222
#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
Has protein modificationY

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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: 3.06 Å3/Da / Density % sol: 59.86 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 6.15
Details: 6% PEG8K, 0.1M Na Citrate, 0.2M NaCl, 1mM ATP, 2mM MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.97901 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 4, 2016
RadiationMonochromator: Silicon (1 1 1) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97901 Å / Relative weight: 1
ReflectionResolution: 2.461→45.252 Å / Num. obs: 27319 / % possible obs: 71.3 % / Redundancy: 18.5 % / Biso Wilson estimate: 75.18 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.024 / Rrim(I) all: 0.105 / Net I/σ(I): 24.3
Reflection shellResolution: 2.461→2.639 Å / Redundancy: 9.3 % / Rmerge(I) obs: 1.622 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1387 / CC1/2: 0.493 / Rpim(I) all: 0.554 / % possible all: 19.4

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHENIX1.19rc6_4061refinement
XDSdata reduction
Aimlessdata scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.461→45.252 Å / SU ML: 0.4348 / Cross valid method: FREE R-VALUE / σ(F): 1.9 / Phase error: 38.9556
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 (27315 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 (27315 reflections). However, separating the reflections on F(+) and F(-), the Phenix program gives a number of 52540 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
Rfree0.2952 1389 5.09 %
Rwork0.2432 49866 -
obs0.2457 27315 71.26 %
Solvent computationShrinkage radii: 1.1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 90.21 Å2
Refinement stepCycle: LAST / Resolution: 2.461→45.252 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5660 0 124 0 5784
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00465874
X-RAY DIFFRACTIONf_angle_d0.76037966
X-RAY DIFFRACTIONf_chiral_restr0.047890
X-RAY DIFFRACTIONf_plane_restr0.00471054
X-RAY DIFFRACTIONf_dihedral_angle_d14.98812250
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 2.76629053776 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.461-2.650.48222040.42592886X-RAY DIFFRACTION20.93
2.65-2.920.3634460.3377890X-RAY DIFFRACTION56.68
2.92-3.340.34375920.319611130X-RAY DIFFRACTION79.52
3.34-4.210.31927440.255813924X-RAY DIFFRACTION99.33
4.21-45.2520.25266880.204114036X-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)
12.032304469490.5537278644030.4949227527922.819486324050.016486080022.01909690590.167386495779-0.1334640798520.3330581650930.007386010850680.4578649788330.120507217892-0.3353368223990.35452816439-0.2200527302780.252181555892-0.06129503124750.2128467384710.416820395623-0.3168037507410.17669902305230.3159952997.6814580397411.266161755
25.94754453149-1.10015520606-0.6922253249690.1300999581340.130774543950.0406066065426-0.140626045911-0.2811506886890.489026272063-0.117186578994-0.4391822609090.102585361082-0.285018003053-0.478614255290.4416690043090.280373997334-0.026888930262-0.0799601574430.895209719352-0.1124303878660.94605745640284.6875504725-4.7582286150914.1192828564
33.061702494111.902780836911.12825960292.44649798909-0.004613545920921.7015928850.570248917956-0.824425460322-0.3185825868810.58726200891-0.6155448053150.4224355044030.407378305602-0.6935640790440.08177662252490.709106453815-0.1030321474910.1789673393991.0436027014-0.1793617238771.0491894435576.3660065391-15.882357953715.1351561482
45.97898576377-1.91826620659-1.612322800472.68620323376-2.156336080667.665103367060.0376160938195-0.165549010135-0.6008299792660.3003478970980.3742542042420.3371010002920.360689749664-0.562561968824-0.3072696329610.499135790178-0.1333295298920.1210562844171.34398121717-0.2644941124121.1903823948875.5441557878-18.86166823746.35113267024
52.63885496515-0.461369710468-1.785303502290.5582530879090.2036780154232.662020361220.0145042042749-0.1308278749820.1402083087160.03231488223980.0247236140480.00265625621603-0.07210607999420.148444075971-0.3231008387680.635665656992-0.1212873623830.4449732374960.768759471351-0.367752026260.79858527436434.481688203713.087246432511.3050367728
62.68920898622-1.22464355667-0.02667263428044.230209010850.3761146813863.575245186610.2061834736610.267147420956-0.694764667609-0.5714704875370.2249406088260.1323737808720.5513396849940.455070539818-0.2820411433690.310767454128-0.0532724114283-0.06068156999960.376585956148-0.1688740320310.24876889535329.2426835251-11.49785445561.67202721258
70.5305434693260.4401067504220.7578183130710.2848795781450.5655448417461.00624338606-0.4821029994880.04950068013370.5499484819690.164084231924-0.4838459093730.004094424329130.180162217165-0.549612190919-0.07735310094010.310882588151-0.1112666888760.2068453843560.6962310421760.03250209618321.3220138505184.4706986913-0.7454934679813.93426431124
86.72016359292-2.529531619960.1129544375751.03567691382-0.2616094740120.189390799644-0.02294977040710.4815943087731.239702885320.0576237844251-0.33652984076-0.334548746522-0.0715424292634-0.1197919744840.2928415326450.591935903694-0.1809279715280.07569620564290.926926856596-0.1670497786480.87100199292175.5875257689.025433432042.32625946465
93.98576446192-3.401938826391.339899210083.99077688203-1.230549284634.797867393490.448265198179-0.004373107492540.0614800236699-0.1024859027880.4151764952310.2476234655060.694154118951-0.326497318388-0.5757252685440.7180196133270.125411438841-0.4904483772471.10635885402-0.3846147697631.7633115445173.430898644511.733014532311.1029000209
104.79597405102-2.6640008913-0.7215779928173.48743715275-0.1522051112472.732269947250.1161102269480.0969573959561-0.572334657355-0.06062920086230.320329331755-0.2164726594670.1414873359920.0636492743081-0.4118185780450.69774689602-0.0736077068999-0.09780201118890.738565857219-0.1471534202530.4752223871132.5209782384-17.47144364341.8957694801
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 176 )AA120 - 176121 - 177
33chain 'A' and (resid 177 through 363 )AA177 - 363178 - 364
44chain 'A' and (resid 401 through 401 )AB401
55chain 'A' and (resid 402 through 402 )AC402
66chain 'B' and (resid 0 through 119 )BD0 - 1191 - 120
77chain 'B' and (resid 120 through 176 )BD120 - 176121 - 177
88chain 'B' and (resid 177 through 363 )BD177 - 363178 - 364
99chain 'B' and (resid 401 through 401 )BE401
1010chain 'B' and (resid 402 through 402 )BF402

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