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- PDB-6rhg: Structure of Chloroflexus aggregans Cagg_3753 LOV domain -

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Basic information

Entry
Database: PDB / ID: 6rhg
TitleStructure of Chloroflexus aggregans Cagg_3753 LOV domain
ComponentsMulti-sensor hybrid histidine kinase
KeywordsFLUORESCENT PROTEIN / LOV / FMN / photoreceptor / flavoprotein
Function / homology
Function and homology information


histidine kinase / phosphorelay sensor kinase activity
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-associated, C-terminal / PAC domain profile. ...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-associated, C-terminal / PAC domain profile. / PAS domain / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / PAS domain / Signal transduction histidine kinase-related protein, C-terminal / 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 / Beta-Lactamase / PAS domain / PAS repeat profile. / PAS domain / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / PAS domain superfamily / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / histidine kinase
Similarity search - Component
Biological speciesChloroflexus aggregans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.22 Å
AuthorsNazarenko, V.V. / Remeeva, A. / Yudenko, A. / Kovalev, K. / Gordeliy, V. / Gushchin, I.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Foundation for Basic Research18-34-00742 Russian Federation
CitationJournal: Photochem. Photobiol. Sci. / Year: 2019
Title: A thermostable flavin-based fluorescent protein from Chloroflexus aggregans: a framework for ultra-high resolution structural studies.
Authors: Nazarenko, V.V. / Remeeva, A. / Yudenko, A. / Kovalev, K. / Dubenko, A. / Goncharov, I.M. / Kuzmichev, P. / Rogachev, A.V. / Buslaev, P. / Borshchevskiy, V. / Mishin, A. / Dhoke, G.V. / ...Authors: Nazarenko, V.V. / Remeeva, A. / Yudenko, A. / Kovalev, K. / Dubenko, A. / Goncharov, I.M. / Kuzmichev, P. / Rogachev, A.V. / Buslaev, P. / Borshchevskiy, V. / Mishin, A. / Dhoke, G.V. / Schwaneberg, U. / Davari, M.D. / Jaeger, K.E. / Krauss, U. / Gordeliy, V. / Gushchin, I.
History
DepositionApr 19, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jul 17, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 24, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _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)26,0557
Polymers24,8662
Non-polymers1,1895
Water4,720262
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-26 kcal/mol
Surface area9900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.790, 110.226, 39.144
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-421-

HOH

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Components

#1: Protein Multi-sensor hybrid histidine kinase


Mass: 12432.947 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
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 262 / Source method: isolated from a natural source / Formula: H2O

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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: 2.33 Å3/Da / Density % sol: 47.29 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.09 M sodium nitrate, 0.09 M sodium phosphate dibasic, 0.09 M ammonium sulfate, 0.1 M imidazole and MES monohydrate (acid) buffer with pH 6.5, 20% PEG 500 MME and 10% 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: 0.976 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.22→48.34 Å / Num. obs: 68182 / % possible obs: 97.4 % / Redundancy: 6.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.04 / Rrim(I) all: 0.102 / Net I/σ(I): 9.4 / Num. measured all: 437195
Reflection shellResolution: 1.22→1.24 Å / Redundancy: 6.6 % / Rmerge(I) obs: 1.419 / Num. unique obs: 3250 / CC1/2: 0.541 / Rpim(I) all: 0.59 / Rrim(I) all: 1.539 / % possible all: 95.6

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Processing

Software
NameVersionClassification
Aimless0.3.11data scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6RHF

6rhf


Resolution: 1.22→48.34 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.536 / SU ML: 0.029 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.037 / ESU R Free: 0.039
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1746 3341 4.9 %RANDOM
Rwork0.1397 ---
obs0.1414 64766 97.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 107.08 Å2 / Biso mean: 19.556 Å2 / Biso min: 10.48 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20 Å20 Å2
2--0.02 Å2-0 Å2
3----0.32 Å2
Refinement stepCycle: final / Resolution: 1.22→48.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1600 0 86 268 1954
Biso mean--16.41 37.69 -
Num. residues----210
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.021878
X-RAY DIFFRACTIONr_bond_other_d0.0010.021763
X-RAY DIFFRACTIONr_angle_refined_deg2.0891.9912600
X-RAY DIFFRACTIONr_angle_other_deg1.45134051
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7255257
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.57324.1392
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.40815281
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.5271519
X-RAY DIFFRACTIONr_chiral_restr0.1350.2297
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0212209
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02442
X-RAY DIFFRACTIONr_rigid_bond_restr8.03633641
X-RAY DIFFRACTIONr_sphericity_free37.013565
X-RAY DIFFRACTIONr_sphericity_bonded12.08153792
LS refinement shellResolution: 1.22→1.252 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 211 -
Rwork0.255 4670 -
all-4881 -
obs--95.26 %

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