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- PDB-9u5v: Structure of Chloroflexus aggregans flavin based fluorescent prot... -

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Basic information

Entry
Database: PDB / ID: 9u5v
TitleStructure of Chloroflexus aggregans flavin based fluorescent protein (CagFbFP) Q89E variant (complex with LC)
Componentshistidine kinase
KeywordsFLUORESCENT PROTEIN / Protein / Fluorescence / Flavin
Function / homology
Function and homology information


phosphorelay sensor kinase activity / histidine kinase / ATP binding / 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 / PAS fold-3 / HPT domain superfamily / 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 / PAS fold-3 / HPT domain superfamily / 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
LUMICHROME / Circadian input-output histidine kinase CikA
Similarity search - Component
Biological speciesChloroflexus aggregans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.663 Å
AuthorsNikolaev, A. / Markeeva, E. / Remeeva, A. / Borshchevsky, V. / Gushchin, I.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Discovery of excited state proton transfer in flavin-based fluorescent protein with large Stokes shift
Authors: Nikolaev, A. / Markeeva, E.
History
DepositionMar 22, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 25, 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: histidine kinase
B: histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2884
Polymers24,8042
Non-polymers4842
Water2,954164
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2340 Å2
ΔGint-16 kcal/mol
Surface area10150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.749, 107.577, 38.932
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-379-

HOH

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Components

#1: Protein histidine kinase


Mass: 12401.867 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chloroflexus aggregans (strain MD-66 / DSM 9485) (bacteria)
Strain: MD-66 / DSM 9485 / Gene: Cagg_3753 / Production host: Escherichia coli (E. coli) / References: UniProt: B8GAY9, histidine kinase
#2: Chemical ChemComp-LUM / LUMICHROME / 7,8-DIMETHYLALLOXAZINE / 6,7-DIMETHYLALLOXAZINE


Mass: 242.233 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H10N4O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / Source method: isolated from a natural source / Formula: H2O
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: 2.27 Å3/Da / Density % sol: 45.79 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Trimethylamine N-oxide dihydrate, 0.1 M Tris pH 8.5, 20% w/v Polyethylene glycol monomethyl ether 2,000

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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 S 16M / Detector: PIXEL / Date: Dec 9, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 1.663→48.099 Å / Num. obs: 19963 / % possible obs: 92.7 % / Redundancy: 7.17 % / CC1/2: 0.996 / Net I/σ(I): 7.9
Reflection shellResolution: 1.663→1.718 Å / Num. unique obs: 910 / CC1/2: 0.581

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
XDSdata reduction
STARANISOdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6RHF

6rhf


Resolution: 1.663→48.099 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.916 / SU B: 2.953 / SU ML: 0.095 / Cross valid method: FREE R-VALUE / ESU R: 0.169 / ESU R Free: 0.157
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2382 856 4.931 %
Rwork0.1892 16503 -
all0.192 --
obs-17359 63.451 %
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: 18.052 Å2
Baniso -1Baniso -2Baniso -3
1--0.129 Å2-0 Å20 Å2
2--0.206 Å2-0 Å2
3----0.077 Å2
Refinement stepCycle: LAST / Resolution: 1.663→48.099 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1592 0 36 164 1792
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0111733
X-RAY DIFFRACTIONr_bond_other_d00.0161637
X-RAY DIFFRACTIONr_angle_refined_deg0.7711.6422381
X-RAY DIFFRACTIONr_angle_other_deg0.2651.5623726
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4955227
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.093518
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.13310251
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.9071084
X-RAY DIFFRACTIONr_chiral_restr0.0360.2267
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022181
X-RAY DIFFRACTIONr_gen_planes_other00.02439
X-RAY DIFFRACTIONr_nbd_refined0.2180.2363
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2130.21517
X-RAY DIFFRACTIONr_nbtor_refined0.1850.2850
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.2825
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2123
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1250.27
X-RAY DIFFRACTIONr_nbd_other0.1990.230
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2150.216
X-RAY DIFFRACTIONr_mcbond_it1.9671.779872
X-RAY DIFFRACTIONr_mcbond_other1.9641.78872
X-RAY DIFFRACTIONr_mcangle_it2.7293.1831093
X-RAY DIFFRACTIONr_mcangle_other2.7283.1851094
X-RAY DIFFRACTIONr_scbond_it3.2472.079861
X-RAY DIFFRACTIONr_scbond_other3.2452.078862
X-RAY DIFFRACTIONr_scangle_it4.7713.6681282
X-RAY DIFFRACTIONr_scangle_other4.773.6671283
X-RAY DIFFRACTIONr_lrange_it5.54118.6332079
X-RAY DIFFRACTIONr_lrange_other5.5418.632080
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.663-1.7060.06710.31416X-RAY DIFFRACTION0.8517
1.706-1.7520.5250.28361X-RAY DIFFRACTION3.4429
1.752-1.8030.40460.27178X-RAY DIFFRACTION9.8029
1.803-1.8580.325190.273382X-RAY DIFFRACTION21.6056
1.858-1.9190.223360.267557X-RAY DIFFRACTION33.5787
1.919-1.9860.296580.237896X-RAY DIFFRACTION56.0188
1.986-2.0610.224750.2251126X-RAY DIFFRACTION71.0651
2.061-2.1450.286770.2181325X-RAY DIFFRACTION87.6798
2.145-2.2410.261670.21392X-RAY DIFFRACTION94.5561
2.241-2.350.238560.2081390X-RAY DIFFRACTION98.838
2.35-2.4760.221660.1841338X-RAY DIFFRACTION98.5263
2.476-2.6260.231610.1971240X-RAY DIFFRACTION97.3074
2.626-2.8070.257680.1861180X-RAY DIFFRACTION98.5004
2.807-3.0310.24560.1921090X-RAY DIFFRACTION97.7816
3.031-3.3190.261530.1991002X-RAY DIFFRACTION95.9964
3.319-3.7080.226450.166929X-RAY DIFFRACTION97.6931
3.708-4.2780.202460.151822X-RAY DIFFRACTION97.2004
4.278-5.2290.117260.135698X-RAY DIFFRACTION95.6407
5.229-7.3520.305160.204557X-RAY DIFFRACTION93.7807
7.352-48.0990.292190.223324X-RAY DIFFRACTION89.7906

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