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- PDB-44oo: Structure of Chloroflexus aggregans Cagg_3753 LOV domain C85A var... -

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Basic information

Entry
Database: PDB / ID: 44oo
TitleStructure of Chloroflexus aggregans Cagg_3753 LOV domain C85A variant (CagFbFP) with 6,7-Dimethyl-8-ribityllumazine
ComponentsCircadian input-output histidine kinase CikA
KeywordsFLUORESCENT PROTEIN / LOV / DLZ / photoreceptor / flavoprotein
Function / homology
Function and homology information


phosphorelay sensor kinase activity / histidine kinase / plasma membrane
Similarity search - Function
PAS fold-4 / PAS fold / Hpt domain / Histidine-containing phosphotransfer (HPt) domain profile. / Signal transduction histidine kinase, phosphotransfer (Hpt) domain / HPT domain superfamily / PAS fold-3 / PAS fold / PAS domain / PAS-associated, C-terminal ...PAS fold-4 / PAS fold / Hpt domain / Histidine-containing phosphotransfer (HPt) domain profile. / Signal transduction histidine kinase, phosphotransfer (Hpt) domain / HPT domain superfamily / PAS fold-3 / PAS fold / 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. / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / 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
Chem-DLZ / Circadian input-output histidine kinase CikA
Similarity search - Component
Biological speciesChloroflexus aggregans DSM 9485 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.274 Å
AuthorsKuznetsova, E. / Semenov, O. / Remeeva, A. / Gushchin, I.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Characterization of LOV domain-ribityllumazine complex with blue-shifted fluorescence
Authors: Kuznetsova, E. / Semenov, O. / Remeeva, A. / Gushchin, I.
History
DepositionAug 6, 2026Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 16, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Circadian input-output histidine kinase CikA
B: Circadian input-output histidine kinase CikA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,17712
Polymers24,8022
Non-polymers1,37510
Water2,900161
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: dimeric
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2890 Å2
ΔGint-59 kcal/mol
Surface area10020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.146, 110.352, 38.906
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-374-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Circadian input-output histidine kinase CikA / Sensory/regulatory protein RpfC


Mass: 12400.882 Da / Num. of mol.: 2 / Mutation: C85A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chloroflexus aggregans DSM 9485 (bacteria)
Gene: Cagg_3753 / Production host: Escherichia coli (E. coli) / References: UniProt: B8GAY9, histidine kinase

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Non-polymers , 5 types, 171 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-DLZ / 1-deoxy-1-(6,7-dimethyl-2,4-dioxo-3,4-dihydropteridin-8(2H)-yl)-D-ribitol / 6,7-dimethyl-8-(1'-D-ribityl) lumazine


Mass: 326.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H18N4O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.34 Å3/Da / Density % sol: 47.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 2.0 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17UM / Wavelength: 0.97919 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Apr 12, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 1.274→55.176 Å / Num. obs: 42328 / % possible obs: 91.9 % / Redundancy: 8.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.046 / Rrim(I) all: 0.139 / Net I/σ(I): 10.4
Reflection shell

Num. unique obs: 2116 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
4.046-55.1768.10.03537.10.9990.0130.03799.2
1.274-1.4134.91.0331.70.6490.4861.14754.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.274→55.176 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.023 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.065 / ESU R Free: 0.067
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2027 2128 5.028 %
Rwork0.1736 40199 -
all0.175 --
obs-42327 68.354 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 11.271 Å2
Baniso -1Baniso -2Baniso -3
1--0.003 Å2-0 Å2-0 Å2
2---0.003 Å2-0 Å2
3---0.005 Å2
Refinement stepCycle: LAST / Resolution: 1.274→55.176 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1600 0 88 161 1849
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0121934
X-RAY DIFFRACTIONr_bond_other_d0.0040.0161831
X-RAY DIFFRACTIONr_angle_refined_deg1.3721.7862678
X-RAY DIFFRACTIONr_angle_other_deg0.7021.7544202
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9495267
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.492522
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.93910289
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.9611095
X-RAY DIFFRACTIONr_chiral_restr0.0810.2308
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022440
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02484
X-RAY DIFFRACTIONr_nbd_refined0.230.2336
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2130.21563
X-RAY DIFFRACTIONr_nbtor_refined0.1790.2911
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.2924
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2133
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0450.28
X-RAY DIFFRACTIONr_nbd_other0.1530.238
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1030.217
X-RAY DIFFRACTIONr_mcbond_it1.291.049934
X-RAY DIFFRACTIONr_mcbond_other1.2791.049934
X-RAY DIFFRACTIONr_mcangle_it1.9361.8831186
X-RAY DIFFRACTIONr_mcangle_other1.9361.8851187
X-RAY DIFFRACTIONr_scbond_it1.9071.2841000
X-RAY DIFFRACTIONr_scbond_other1.9061.2841001
X-RAY DIFFRACTIONr_scangle_it2.8132.2561470
X-RAY DIFFRACTIONr_scangle_other2.8122.2561471
X-RAY DIFFRACTIONr_lrange_it4.13211.6512191
X-RAY DIFFRACTIONr_lrange_other4.13111.6492191
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.274-1.3070.41420.322710.32445260.9950.9371.61290.318
1.307-1.3420.298190.263190.26244120.9350.9557.66090.251
1.342-1.3810.317450.2557560.25942760.9410.95418.73250.251
1.381-1.4240.27670.25211990.25341610.950.95830.42540.244
1.424-1.470.252690.2315300.23140050.9610.96439.92510.221
1.47-1.5220.2411200.23122990.23139230.9590.96361.6620.216
1.522-1.5790.2251790.23131310.2337930.9660.96387.2660.212
1.579-1.6440.2651910.20633550.20936480.9520.96997.20390.182
1.644-1.7170.2281890.19232760.19434990.9650.97499.02830.169
1.717-1.8010.2321700.17531630.17833580.9710.97999.25550.152
1.801-1.8980.1971410.15430280.15531870.9740.98599.43520.135
1.898-2.0130.1821430.15128580.15230350.9820.98698.87970.134
2.013-2.1520.1771400.14726870.14928620.9810.98798.77710.132
2.152-2.3240.1791240.15225130.15326440.9790.98699.73520.139
2.324-2.5450.1871240.14523440.14724690.9770.98799.95950.133
2.545-2.8450.167930.15221510.15322450.9810.98599.95550.14
2.845-3.2830.2031150.16118620.16420020.9740.98498.75120.156
3.283-4.0180.217830.16816120.17117010.9710.98399.64730.166
4.018-5.6670.142760.16712770.16513620.990.98499.33920.175
5.667-55.1760.324380.2927680.2948150.9590.9698.89570.322

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