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

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Basic information

Entry
Database: PDB / ID: 6yxb
TitleStructure of Chloroflexus aggregans flavin based fluorescent protein (CagFbFP) Q148K variant (space group P21)
ComponentsMulti-sensor hybrid histidine kinase
KeywordsFLUORESCENT PROTEIN / LOV domain
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 / Histidine kinase/HSP90-like ATPase / PAS domain ...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 / Histidine kinase/HSP90-like ATPase / 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 superfamily
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Circadian input-output histidine kinase CikA
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: J.Biol.Chem. / Year: 2021
Title: The molecular basis of spectral tuning in blue- and red-shifted flavin-binding fluorescent proteins.
Authors: Rollen, K. / Granzin, J. / Remeeva, A. / Davari, M.D. / Gensch, T. / Nazarenko, V.V. / Kovalev, K. / Bogorodskiy, A. / Borshchevskiy, V. / Hemmer, S. / Schwaneberg, U. / Gordeliy, V. / ...Authors: Rollen, K. / Granzin, J. / Remeeva, A. / Davari, M.D. / Gensch, T. / Nazarenko, V.V. / Kovalev, K. / Bogorodskiy, A. / Borshchevskiy, V. / Hemmer, S. / Schwaneberg, U. / Gordeliy, V. / Jaeger, K.E. / Batra-Safferling, R. / Gushchin, I. / Krauss, U.
#1: 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.
#2: 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.
#3: Journal: Biorxiv / Year: 2021
Title: Structural and mechanistic insight into spectral tuning in flavin-binding fluorescent proteins
Authors: Rollen, K. / Granzin, J. / Remeeva, A. / Davari, M.D. / Gensch, T. / Nazarenko, V.V. / Kovalev, K. / Bogorodskiy, A. / Borshchevskiy, V. / Hemmer, S. / Schwaneberg, U. / Gordeliy, V. / ...Authors: Rollen, K. / Granzin, J. / Remeeva, A. / Davari, M.D. / Gensch, T. / Nazarenko, V.V. / Kovalev, K. / Bogorodskiy, A. / Borshchevskiy, V. / Hemmer, S. / Schwaneberg, U. / Gordeliy, V. / Jaeger, K.E. / Batra-Safferling, R. / Gushchin, I. / Krauss, U.
History
DepositionApr 30, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 21, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2021Group: Database references / Category: citation / citation_author
Item: _citation.id / _citation.journal_abbrev ..._citation.id / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.citation_id / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jul 21, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Jan 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
C: Multi-sensor hybrid histidine kinase
D: Multi-sensor hybrid histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,91313
Polymers49,6084
Non-polymers2,3069
Water8,377465
1
A: Multi-sensor hybrid histidine kinase
B: Multi-sensor hybrid histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9096
Polymers24,8042
Non-polymers1,1054
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3540 Å2
ΔGint-47 kcal/mol
Surface area9910 Å2
MethodPISA
2
C: Multi-sensor hybrid histidine kinase
D: Multi-sensor hybrid histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0057
Polymers24,8042
Non-polymers1,2015
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3720 Å2
ΔGint-58 kcal/mol
Surface area9870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.101, 110.538, 56.941
Angle α, β, γ (deg.)90.000, 91.070, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Multi-sensor hybrid histidine kinase


Mass: 12401.934 Da / Num. of mol.: 4 / Mutation: Q148K
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.: 4 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 465 / 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: 2.48 Å3/Da / Density % sol: 50.41 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.5M Ammonium Sulfate, 0.1M tri-Sodium citrate, pH 6.5, 1M Lithium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9737 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9737 Å / Relative weight: 1
ReflectionResolution: 1.5→110.54 Å / Num. obs: 76240 / % possible obs: 98.9 % / Redundancy: 3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.049 / Rrim(I) all: 0.087 / Net I/σ(I): 10.6 / Num. measured all: 228792 / Scaling rejects: 300
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
1.5-1.5330.4841106437060.6760.3320.5892.698.1
8.22-110.542.90.03814044800.9980.0260.04725.596.3

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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: 6yx4

6yx4


Resolution: 1.5→56.95 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.946 / SU B: 1.353 / SU ML: 0.05 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.073 / ESU R Free: 0.072
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2029 3694 4.8 %RANDOM
Rwork0.1836 ---
obs0.1845 72508 98.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 51.51 Å2 / Biso mean: 12.813 Å2 / Biso min: 5.52 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å2-0 Å20.15 Å2
2---0.26 Å2-0 Å2
3---0.22 Å2
Refinement stepCycle: final / Resolution: 1.5→56.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3152 0 149 471 3772
Biso mean--11.68 25.78 -
Num. residues----416
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0133482
X-RAY DIFFRACTIONr_bond_other_d00.0173192
X-RAY DIFFRACTIONr_angle_refined_deg1.2961.7034804
X-RAY DIFFRACTIONr_angle_other_deg1.2971.6017370
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5675454
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.25421.224196
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.05115514
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.841535
X-RAY DIFFRACTIONr_chiral_restr0.0490.2473
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023961
X-RAY DIFFRACTIONr_gen_planes_other00.02752
LS refinement shellResolution: 1.5→1.539 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 262 -
Rwork0.269 5320 -
all-5582 -
obs--98.31 %

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