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- PDB-7oo9: Structure of Chloroflexus islandicus LOV domain C85A variant (CisFbFP) -

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Basic information

Entry
Database: PDB / ID: 7oo9
TitleStructure of Chloroflexus islandicus LOV domain C85A variant (CisFbFP)
ComponentsHybrid sensor histidine kinase/response regulator
KeywordsFLUORESCENT PROTEIN / Flavin
Function / homology
Function and homology information


phosphorelay sensor kinase activity / 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 / HPT domain superfamily / PAS fold-3 / PAS fold / PAS-associated, C-terminal / PAS domain ...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 / PAS domain / PAC domain profile. / 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. / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / PAS domain / PAS domain superfamily / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Hybrid sensor histidine kinase/response regulator
Similarity search - Component
Biological speciesChloroflexus islandicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsGushchin, I. / Remeeva, A. / Goncharov, I.M.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Science Foundation21-64-00018 Russian Federation
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2021
Title: High-resolution structure of a naturally red-shifted LOV domain.
Authors: Goncharov, I.M. / Smolentseva, A. / Semenov, O. / Natarov, I. / Nazarenko, V.V. / Yudenko, A. / Remeeva, A. / Gushchin, I.
History
DepositionMay 26, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 30, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 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: Hybrid sensor histidine kinase/response regulator
B: Hybrid sensor histidine kinase/response regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,94814
Polymers25,1142
Non-polymers1,83412
Water4,810267
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5330 Å2
ΔGint-31 kcal/mol
Surface area10320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.606, 62.541, 64.157
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Hybrid sensor histidine kinase/response regulator


Mass: 12557.126 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chloroflexus islandicus (bacteria) / Gene: A6A03_05810 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A178LR65
#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.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 267 / 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: 2.46 Å3/Da / Density % sol: 50.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.04 M KH2PO4, 16% w/v PEG 8000, 20% v/v glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 14, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.2→64.16 Å / Num. obs: 77945 / % possible obs: 99.8 % / Redundancy: 6.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.031 / Rrim(I) all: 0.075 / Net I/σ(I): 12.3 / Num. measured all: 474237 / Scaling rejects: 66
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
1.2-1.225.70.9312143337900.7760.4261.0261.899.4
6.57-64.165.30.05130435720.9940.0250.05824.899.8

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6RHF

6rhf


Resolution: 1.2→44.78 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.157 / SU ML: 0.023 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.038 / ESU R Free: 0.038 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1846 4048 5.2 %RANDOM
Rwork0.1577 ---
obs0.1592 73725 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 87.54 Å2 / Biso mean: 13.723 Å2 / Biso min: 7.52 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å20 Å2-0 Å2
2---0.27 Å20 Å2
3----0.22 Å2
Refinement stepCycle: final / Resolution: 1.2→44.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1628 0 131 271 2030
Biso mean--18.88 27.62 -
Num. residues----212
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0131900
X-RAY DIFFRACTIONr_bond_other_d0.0180.0171774
X-RAY DIFFRACTIONr_angle_refined_deg2.0521.7012608
X-RAY DIFFRACTIONr_angle_other_deg1.5721.5974103
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9375245
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.09120.392102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.3115274
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0731519
X-RAY DIFFRACTIONr_chiral_restr0.1140.2250
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.022116
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02417
X-RAY DIFFRACTIONr_rigid_bond_restr5.43533672
LS refinement shellResolution: 1.2→1.231 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 288 -
Rwork0.323 5373 -
all-5661 -
obs--99.42 %

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