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- PDB-5dkk: Structure of the dark-state monomer of the blue light photorecept... -

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Basic information

Entry
Database: PDB / ID: 5dkk
TitleStructure of the dark-state monomer of the blue light photoreceptor Aureochrome 1a LOV from P. tricornutum
ComponentsLOV domainLight-oxygen-voltage-sensing domain
KeywordsSIGNALING PROTEIN / LOV DNA binding photoreceptor / flavoprotein / transcription
Function / homology
Function and homology information


PAS-associated, C-terminal / PAS domain / PAC domain profile. / PAS domain / Beta-Lactamase / PAS repeat profile. / PAS domain / PAS domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / FLAVIN MONONUCLEOTIDE / LOV domain-containing protein
Similarity search - Component
Biological speciesPhaeodactylum tricornutum (Diatom)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsHeintz, U. / Schlichting, I.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationFOR526 Germany
CitationJournal: Elife / Year: 2016
Title: Blue light-induced LOV domain dimerization enhances the affinity of Aureochrome 1a for its target DNA sequence.
Authors: Heintz, U. / Schlichting, I.
History
DepositionSep 3, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2016Group: Database references
Revision 1.2Jul 27, 2016Group: Database references
Revision 1.3Jan 10, 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

Downloads & links

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Assembly

Deposited unit
A: LOV domain
B: LOV domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1047
Polymers32,0112
Non-polymers1,0935
Water99155
1
A: LOV domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6425
Polymers16,0061
Non-polymers6374
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: LOV domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4622
Polymers16,0061
Non-polymers4561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.370, 69.210, 74.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein LOV domain / Light-oxygen-voltage-sensing domain


Mass: 16005.620 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phaeodactylum tricornutum (Diatom) / Plasmid: pETM-11 / Production host: Escherichia coli (E. coli) / References: UniProt: B7G9J2*PLUS
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: 40% (v/v) ethylene glycol, 0.1 M sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 2, 2014
RadiationMonochromator: Si-111 and Si-113 reflection / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 12016 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 13.1 % / Rmerge(I) obs: 0.127 / Net I/σ(I): 15.57
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 13.5 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 4.5 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ue6, chain A and residues 219-317

3ue6


Resolution: 2.5→48.735 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / Phase error: 24.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2536 962 8.01 %
Rwork0.1956 --
obs0.2003 12016 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→48.735 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2108 0 74 55 2237
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072220
X-RAY DIFFRACTIONf_angle_d1.1093019
X-RAY DIFFRACTIONf_dihedral_angle_d12.595807
X-RAY DIFFRACTIONf_chiral_restr0.05330
X-RAY DIFFRACTIONf_plane_restr0.007399
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5002-2.6320.27471340.20251544X-RAY DIFFRACTION100
2.632-2.79690.26071360.21031554X-RAY DIFFRACTION100
2.7969-3.01280.28121350.2171551X-RAY DIFFRACTION100
3.0128-3.31590.28041350.21331557X-RAY DIFFRACTION100
3.3159-3.79560.23551370.20181577X-RAY DIFFRACTION100
3.7956-4.78140.23851390.16991595X-RAY DIFFRACTION100
4.7814-48.74440.25171460.19361676X-RAY DIFFRACTION100

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