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- PDB-6y7u: Structure of Chloroflexus aggregans Cagg_3753 LOV domain C85A A95... -

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Basic information

Entry
Database: PDB / ID: 6y7u
TitleStructure of Chloroflexus aggregans Cagg_3753 LOV domain C85A A95P variant (CagFbFP)
ComponentsMulti-sensor hybrid histidine kinase
KeywordsFLUORESCENT PROTEIN / LOV domain / flavoprotein
Function / homology
Function and homology information


histidine kinase / phosphorelay sensor kinase activity / nucleotide binding / plasma membrane
Similarity search - Function
PAS fold-4 / PAS fold / PAS fold-3 / Hpt domain / Histidine-containing phosphotransfer (HPt) domain profile. / Signal transduction histidine kinase, phosphotransfer (Hpt) domain / HPT domain superfamily / PAS fold / PAS domain / PAS-associated, C-terminal ...PAS fold-4 / PAS fold / PAS fold-3 / Hpt domain / Histidine-containing phosphotransfer (HPt) domain profile. / Signal transduction histidine kinase, phosphotransfer (Hpt) domain / 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) / PAS 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 / Beta-Lactamase / PAS domain / PAS repeat profile. / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / PAS domain / Histidine kinase-like ATPases / PAS domain superfamily / 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
Water3,945219
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 area9980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.256, 111.360, 38.935
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-404-

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


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / 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: 2.37 Å3/Da / Density % sol: 48.02 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Ammonium sulfate, 0.1 M BIS-Tris pH 5.5, 25 % w/v PEG 3350

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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→111.36 Å / Num. obs: 31994 / % possible obs: 99.9 % / Redundancy: 10.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.032 / Rrim(I) all: 0.106 / Net I/σ(I): 14 / Num. measured all: 336840 / Scaling rejects: 16
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 11.1 % / Rmerge(I) obs: 0.685 / Num. unique obs: 1582 / CC1/2: 0.928 / Rpim(I) all: 0.215 / Rrim(I) all: 0.719 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6rhf

6rhf


Resolution: 1.6→38.97 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.935 / SU B: 4.036 / SU ML: 0.064 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.114 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2247 1547 4.8 %RANDOM
Rwork0.1784 ---
obs0.1806 30392 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 67.58 Å2 / Biso mean: 18.887 Å2 / Biso min: 9.77 Å2
Baniso -1Baniso -2Baniso -3
1-1.63 Å20 Å20 Å2
2---0.07 Å20 Å2
3----1.56 Å2
Refinement stepCycle: final / Resolution: 1.6→38.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1603 0 62 221 1886
Biso mean--15.84 30.8 -
Num. residues----211
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0131783
X-RAY DIFFRACTIONr_bond_other_d0.0020.0171618
X-RAY DIFFRACTIONr_angle_refined_deg1.3141.7082454
X-RAY DIFFRACTIONr_angle_other_deg1.2871.6023733
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.795229
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.89921.068103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.23115256
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5891519
X-RAY DIFFRACTIONr_chiral_restr0.0530.2243
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022052
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02389
X-RAY DIFFRACTIONr_rigid_bond_restr4.58333401
LS refinement shellResolution: 1.6→1.642 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 99 -
Rwork0.213 2228 -
all-2327 -
obs--99.96 %

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