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- PDB-5a8b: Structure of a parallel dimer of the aureochrome 1a LOV domain fr... -

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Basic information

Entry
Database: PDB / ID: 5a8b
TitleStructure of a parallel dimer of the aureochrome 1a LOV domain from Phaeodactylum tricornutum
ComponentsPTAUREO1A LOV2 DOMAIN
KeywordsUNKNOWN FUNCTION / AUREOCHROME 1 / PARALLEL LOV DIMER AND FLANKING HELIX.
Function / homology
Function and homology information


nucleotide binding / nucleus
Similarity search - Function
PAS domain / PAS-associated, C-terminal / PAC domain profile. / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / PAS domain / Beta-Lactamase / PAS repeat profile. / PAS domain / PAS domain superfamily ...PAS domain / PAS-associated, C-terminal / PAC domain profile. / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / PAS domain / Beta-Lactamase / PAS repeat profile. / PAS domain / PAS domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Ptaureo1a lov2 domain
Similarity search - Component
Biological speciesPHAEODACTYLUM TRICORNUTUM (Diatom)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.791 Å
AuthorsBanerjee, A. / Herman, E. / Kottke, T. / Essen, L.O.
CitationJournal: Structure / Year: 2016
Title: Structure of a Native-like Aureochrome 1a LOV Domain Dimer from Phaeodactylum tricornutum.
Authors: Ankan Banerjee / Elena Herman / Tilman Kottke / Lars-Oliver Essen /
Abstract: Light-oxygen-voltage (LOV) domains absorb blue light for mediating various biological responses in all three domains of life. Aureochromes from stramenopile algae represent a subfamily of ...Light-oxygen-voltage (LOV) domains absorb blue light for mediating various biological responses in all three domains of life. Aureochromes from stramenopile algae represent a subfamily of photoreceptors that differs by its inversed topology with a C-terminal LOV sensor and an N-terminal effector (basic region leucine zipper, bZIP) domain. We crystallized the LOV domain including its flanking helices, A'α and Jα, of aureochrome 1a from Phaeodactylum tricornutum in the dark state and solved the structure at 2.8 Å resolution. Both flanking helices contribute to the interface of the native-like dimer. Small-angle X-ray scattering shows light-induced conformational changes limited to the dimeric envelope as well as increased flexibility in the lit state for the flanking helices. These rearrangements are considered to be crucial for the formation of the light-activated dimer. Finally, the LOV domain of the class 2 aureochrome PtAUREO2 was shown to lack a chromophore because of steric hindrance caused by M301.
History
DepositionJul 14, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 10, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PTAUREO1A LOV2 DOMAIN
B: PTAUREO1A LOV2 DOMAIN
C: PTAUREO1A LOV2 DOMAIN
D: PTAUREO1A LOV2 DOMAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,95611
Polymers71,9674
Non-polymers1,9887
Water57632
1
A: PTAUREO1A LOV2 DOMAIN
B: PTAUREO1A LOV2 DOMAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9325
Polymers35,9842
Non-polymers9483
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3810 Å2
ΔGint-30.3 kcal/mol
Surface area12570 Å2
MethodPISA
2
C: PTAUREO1A LOV2 DOMAIN
D: PTAUREO1A LOV2 DOMAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0246
Polymers35,9842
Non-polymers1,0404
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3920 Å2
ΔGint-25.4 kcal/mol
Surface area13030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.391, 75.550, 77.664
Angle α, β, γ (deg.)90.00, 94.73, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
PTAUREO1A LOV2 DOMAIN


Mass: 17991.809 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: 1GOL / Source: (gene. exp.) PHAEODACTYLUM TRICORNUTUM (Diatom) / Strain: CCAP3/55 UTEX646 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): LYSE / References: UniProt: A0A140UHJ0*PLUS
#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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsJGI ID-49116

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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: 2.32 Å3/Da / Density % sol: 46.9 % / Description: NONE
Crystal growpH: 8 / Details: 24%(W/V) PEG1500, 20%(V/V) GLYCEROL, pH 8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.3 / Wavelength: 0.91841
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 19, 2014 / Details: MIRRORS
RadiationMonochromator: KMC-3 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.79→38.7 Å / Num. obs: 16065 / % possible obs: 98.9 % / Observed criterion σ(I): 10 / Redundancy: 4.1 % / Biso Wilson estimate: 32.16 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 8.5
Reflection shellResolution: 2.79→2.97 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 308 / % possible all: 94.3

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3UE6

3ue6


Resolution: 2.791→38.7 Å / SU ML: 0.35 / σ(F): 1.36 / Phase error: 22.08 / Stereochemistry target values: ML / Details: DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY
RfactorNum. reflection% reflection
Rfree0.23 794 4.9 %
Rwork0.1703 --
obs0.1733 16065 98.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.791→38.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4150 0 132 32 4314
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094372
X-RAY DIFFRACTIONf_angle_d1.2085957
X-RAY DIFFRACTIONf_dihedral_angle_d17.2671565
X-RAY DIFFRACTIONf_chiral_restr0.055653
X-RAY DIFFRACTIONf_plane_restr0.006779
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7914-2.96620.27841360.20572411X-RAY DIFFRACTION94
2.9662-3.19510.27811280.20982543X-RAY DIFFRACTION100
3.1951-3.51650.2661380.18572574X-RAY DIFFRACTION100
3.5165-4.02480.21651310.16542578X-RAY DIFFRACTION100
4.0248-5.06910.19971270.13832560X-RAY DIFFRACTION99
5.0691-38.70380.19811340.16342606X-RAY DIFFRACTION99

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