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- PDB-7ab7: Structure of Chloroflexus aggregans flavin based fluorescent prot... -

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Basic information

Entry
Database: PDB / ID: 7ab7
TitleStructure of Chloroflexus aggregans flavin based fluorescent protein (CagFbFP) I52T Q148K variant
ComponentsMulti-sensor hybrid histidine kinase
KeywordsFLUORESCENT PROTEIN / LOV domain
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 / 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 / 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
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / histidine kinase
Similarity search - Component
Biological speciesChloroflexus aggregans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsRemeeva, A. / Nazarenko, V. / Kovalev, K. / Gushchin, I.
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: 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
DepositionSep 6, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 21, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2021Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 21, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Jan 31, 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)25,9737
Polymers24,7802
Non-polymers1,1935
Water3,153175
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3560 Å2
ΔGint-33 kcal/mol
Surface area10250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.083, 111.992, 39.031
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-391-

HOH

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Components

#1: Protein Multi-sensor hybrid histidine kinase


Mass: 12389.880 Da / Num. of mol.: 2 / Mutation: I52T 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 / Flavin mononucleotide


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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 175 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.56 Å3/Da / Density % sol: 51.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M Lithium sulfate 0.1M BIS-Tris pH 5.5 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.8→53.08 Å / Num. obs: 22158 / % possible obs: 99.5 % / Redundancy: 3.3 % / CC1/2: 0.996 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.049 / Rrim(I) all: 0.092 / Net I/σ(I): 7.1 / Num. measured all: 72891 / 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
1.8-1.843.30.568431812930.7450.3610.6761.599.8
9-53.0830.0376162050.9960.0240.04517.494.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
Aimless0.3.11data scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6RHF

6rhf


Resolution: 1.8→48.01 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.815 / SU ML: 0.085 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.114 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1947 1110 5 %RANDOM
Rwork0.1587 ---
obs0.1606 21021 99.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 68.67 Å2 / Biso mean: 21.224 Å2 / Biso min: 12.16 Å2
Baniso -1Baniso -2Baniso -3
1-0.9 Å20 Å20 Å2
2--0.27 Å2-0 Å2
3----1.17 Å2
Refinement stepCycle: final / Resolution: 1.8→48.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1598 0 79 180 1857
Biso mean--20.14 33.6 -
Num. residues----210
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0131873
X-RAY DIFFRACTIONr_bond_other_d0.0030.0171703
X-RAY DIFFRACTIONr_angle_refined_deg1.7161.7072596
X-RAY DIFFRACTIONr_angle_other_deg1.4421.6053951
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2075254
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.82921.339112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.93115281
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0111520
X-RAY DIFFRACTIONr_chiral_restr0.080.2258
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022176
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02412
LS refinement shellResolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 90 -
Rwork0.233 1522 -
all-1612 -
obs--99.44 %

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