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- PDB-6y7r: Structure of Chloroflexus aggregans Cagg_3753 LOV domain C85A A56... -

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Basic information

Entry
Database: PDB / ID: 6y7r
TitleStructure of Chloroflexus aggregans Cagg_3753 LOV domain C85A A56P variant (CagFbFP)
ComponentsMulti-sensor hybrid histidine kinase
KeywordsFLUORESCENT PROTEIN / LOV domain / 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: 1.6 Å
AuthorsRemeeva, A. / Nazarenko, V. / Kovalev, K. / Gordeliy, V. / Gushchin, I.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Science Foundation18-74-00092 Russian Federation
CitationJournal: Crystals / Year: 2020
Title: Effects of Proline Substitutions on the Thermostable LOV Domain from Chloroflexus aggregans
Authors: Remeeva, A. / Nazarenko, V.V. / Goncharov, I.M. / Yudenko, A. / Smolentseva, A. / Semenov, O. / Kovalev, K. / Gulbahar, C. / Schwaneberg, U. / Davari, M.D. / Gordeliy, V. / Gushchin, I.
History
DepositionMar 2, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 22, 2020Provider: 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 / database_2 / pdbx_initial_refinement_model
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)25,7674
Polymers24,8542
Non-polymers9132
Water4,972276
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3050 Å2
ΔGint-25 kcal/mol
Surface area10030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.585, 111.289, 39.220
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-420-

HOH

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Components

#1: Protein Multi-sensor hybrid histidine kinase


Mass: 12426.919 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chloroflexus aggregans (strain MD-66 / DSM 9485) (bacteria)
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 276 / 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: 2.4 Å3/Da / Density % sol: 48.68 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Ammonium acetate, 0.1 M BIS-Tris pH 5.5, 17 % w/v PEG 10000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.976 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.6→111.29 Å / Num. obs: 32415 / % possible obs: 100 % / Redundancy: 13.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.033 / Rrim(I) all: 0.119 / Net I/σ(I): 14.5 / Num. measured all: 425485 / Scaling rejects: 1
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 13.3 % / Rmerge(I) obs: 1.628 / Num. unique obs: 1580 / CC1/2: 0.761 / Rpim(I) all: 0.465 / Rrim(I) all: 1.694 / % possible all: 100

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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: 1.6→39.25 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.942 / SU B: 1.857 / SU ML: 0.064 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.091 / ESU R Free: 0.09
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.214 1563 4.8 %RANDOM
Rwork0.184 ---
obs0.1854 30768 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 74.06 Å2 / Biso mean: 19.52 Å2 / Biso min: 9.08 Å2
Baniso -1Baniso -2Baniso -3
1-1.18 Å20 Å20 Å2
2---0.38 Å20 Å2
3----0.81 Å2
Refinement stepCycle: final / Resolution: 1.6→39.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1607 0 62 283 1952
Biso mean--15.89 33.83 -
Num. residues----211
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0131826
X-RAY DIFFRACTIONr_bond_other_d00.0171650
X-RAY DIFFRACTIONr_angle_refined_deg1.2841.7062521
X-RAY DIFFRACTIONr_angle_other_deg1.2651.6033818
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5585241
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.1721.111108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.94415266
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6181520
X-RAY DIFFRACTIONr_chiral_restr0.0480.2249
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022126
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02402
LS refinement shellResolution: 1.6→1.641 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 104 -
Rwork0.279 2256 -
all-2360 -
obs--99.92 %

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