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

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Basic information

Entry
Database: PDB / ID: 6ywr
TitleStructure of Chloroflexus aggregans flavin based fluorescent protein (CagFbFP) Q148H variant (space group C2)
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 / histidine kinase
Similarity search - Component
Biological speciesChloroflexus aggregans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 30, 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
B: Multi-sensor hybrid histidine kinase
A: Multi-sensor hybrid histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1198
Polymers24,8222
Non-polymers1,2976
Water3,135174
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-65 kcal/mol
Surface area10290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.967, 54.035, 39.229
Angle α, β, γ (deg.)90.000, 98.500, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Multi-sensor hybrid histidine kinase


Mass: 12410.900 Da / Num. of mol.: 2 / Mutation: Q148H
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
#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-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 174 / Source method: isolated from a natural source / Formula: H2O
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: 47.5 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.5 M Lithium sulfate monohydrate, 15% w/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.5→54.87 Å / Num. obs: 35488 / % possible obs: 96.4 % / Redundancy: 3.2 % / CC1/2: 0.995 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.046 / Rrim(I) all: 0.085 / Net I/σ(I): 9.5 / Num. measured all: 114941 / Scaling rejects: 5
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
1.5-1.533.20.49578417850.7530.3180.5862.399.2
8.22-54.872.90.0636942370.9920.0420.07720.197.1

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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: 1.5→54.87 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.43 / SU ML: 0.053 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.076 / ESU R Free: 0.075
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1998 1798 5.1 %RANDOM
Rwork0.176 ---
obs0.1772 33688 96.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 65.55 Å2 / Biso mean: 16.478 Å2 / Biso min: 8.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.38 Å2-0 Å2-0.25 Å2
2---0.03 Å2-0 Å2
3----0.26 Å2
Refinement stepCycle: final / Resolution: 1.5→54.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1599 0 82 176 1857
Biso mean--18.88 28.99 -
Num. residues----211
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0131860
X-RAY DIFFRACTIONr_bond_other_d00.0171668
X-RAY DIFFRACTIONr_angle_refined_deg1.3231.6972580
X-RAY DIFFRACTIONr_angle_other_deg1.3111.5963867
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4015248
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.16421.748103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg1215262
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.8361516
X-RAY DIFFRACTIONr_chiral_restr0.0540.2253
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022144
X-RAY DIFFRACTIONr_gen_planes_other00.02396
LS refinement shellResolution: 1.5→1.539 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 126 -
Rwork0.244 2550 -
all-2676 -
obs--99.18 %

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