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- PDB-6ywh: Structure of Chloroflexus aggregans flavin based fluorescent prot... -

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Basic information

Entry
Database: PDB / ID: 6ywh
TitleStructure of Chloroflexus aggregans flavin based fluorescent protein (CagFbFP) Q148D variant
ComponentsMulti-sensor hybrid histidine kinase
KeywordsFLUORESCENT PROTEIN / LOV domain
Function / homology
Function and homology information


histidine kinase / phosphorelay sensor kinase activity / nucleotide 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
FLAVIN MONONUCLEOTIDE / TRIETHYLENE GLYCOL / histidine kinase
Similarity search - Component
Biological speciesChloroflexus aggregans DSM 9485 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.07 Å
AuthorsRemeeva, A. / Nazarenko, V. / Kovalev, K. / Gushchin, I.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Science Foundation18-74-00092 Russian Federation
Citation
Journal: Proteins / Year: 2021
Title: Insights into the mechanisms of light-oxygen-voltage domain color tuning from a set of high-resolution X-ray structures.
Authors: Remeeva, A. / Nazarenko, V.V. / Kovalev, K. / Goncharov, I.M. / Yudenko, A. / Astashkin, R. / Gordeliy, V. / Gushchin, I.
#1: Journal: Biorxiv / Year: 2021
Title: Insights into the mechanisms of LOV domain color tuning from a set of high-resolution X-ray structures
Authors: Remeeva, A. / Nazarenko, V.V. / Kovalev, K. / Goncharov, I. / Yudenko, A. / Astashkin, R. / Gordeliy, V. / Gushchin, I.
History
DepositionApr 29, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 21, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Multi-sensor hybrid histidine kinase
B: Multi-sensor hybrid histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2287
Polymers24,7762
Non-polymers1,4525
Water3,801211
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3740 Å2
ΔGint-23 kcal/mol
Surface area10670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.661, 110.471, 39.043
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-390-

HOH

21B-404-

HOH

31B-406-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Multi-sensor hybrid histidine kinase


Mass: 12387.841 Da / Num. of mol.: 2 / Mutation: Q148D
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

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Non-polymers , 5 types, 216 molecules

#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 47.33 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.1 M DL-Glutamic acid monohydrate, 0.1 M DL-Alanine, 0.1 M Glycine, 0.1 M DL-Lysine monohydrochloride, 0.1 M DL-Serine, 0.1M MES monohydrate, 0.1M Imidazole, pH 6.5, 20% v/v PEG 500 MME, 10% w/v PEG 20000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 1.07→55.24 Å / Num. obs: 101277 / % possible obs: 98.4 % / Redundancy: 6.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.019 / Rrim(I) all: 0.048 / Net I/σ(I): 16.1 / Num. measured all: 644391 / Scaling rejects: 1
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
1.07-1.0960.9673002749700.6650.4251.059298.3
5.86-55.246.10.02845477470.9990.0120.03150.899.8

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6rhf

6rhf


Resolution: 1.07→48.31 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.97 / SU B: 0.442 / SU ML: 0.022 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.029 / ESU R Free: 0.03
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1884 5119 5.1 %RANDOM
Rwork0.1761 ---
obs0.1767 96086 98.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 56.9 Å2 / Biso mean: 13.203 Å2 / Biso min: 7.41 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20 Å20 Å2
2---0.07 Å20 Å2
3----0.27 Å2
Refinement stepCycle: final / Resolution: 1.07→48.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1614 0 91 217 1922
Biso mean--17.8 25.18 -
Num. residues----212
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0131860
X-RAY DIFFRACTIONr_bond_other_d00.0171691
X-RAY DIFFRACTIONr_angle_refined_deg1.4421.7022567
X-RAY DIFFRACTIONr_angle_other_deg1.4431.6013926
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9965247
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.67521.532111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.84815269
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.911519
X-RAY DIFFRACTIONr_chiral_restr0.0660.2253
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022129
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02400
LS refinement shellResolution: 1.07→1.098 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 372 -
Rwork0.27 7016 -
all-7388 -
obs--98.17 %

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