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- PDB-6i23: Flavin Analogue Sheds Light on Light-Oxygen-Voltage Domain Mechanism -

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Basic information

Entry
Database: PDB / ID: 6i23
TitleFlavin Analogue Sheds Light on Light-Oxygen-Voltage Domain Mechanism
Components(Aureochrome1-like ...) x 2
KeywordsTRANSCRIPTION / LOV Domain / FMN / Dark grown / fluorescence / light sensing / transcription factor PAS domain / Ochronomas danica
Function / homology
Function and homology information


DNA-binding transcription factor activity / nucleotide binding / metal ion binding / nucleus
Similarity search - Function
Basic region leucine zipper / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Basic-leucine zipper domain / Basic-leucine zipper 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) ...Basic region leucine zipper / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Basic-leucine zipper domain / Basic-leucine zipper 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
Chem-9O9 / ACETATE ION / Aureochrome1-like protein
Similarity search - Component
Biological speciesOchromonas danica (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsRizkallah, P.J. / Kalvaitis, M.E. / Allemann, R.K. / Mart, R.J. / Johnson, L.A.
CitationJournal: Biochemistry / Year: 2019
Title: A Noncanonical Chromophore Reveals Structural Rearrangements of the Light-Oxygen-Voltage Domain upon Photoactivation.
Authors: Kalvaitis, M.E. / Johnson, L.A. / Mart, R.J. / Rizkallah, P. / Allemann, R.K.
History
DepositionOct 31, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 29, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 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

Downloads & links

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Assembly

Deposited unit
A: Aureochrome1-like protein
B: Aureochrome1-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,80415
Polymers29,1372
Non-polymers1,66713
Water2,288127
1
A: Aureochrome1-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1187
Polymers14,3821
Non-polymers7366
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Aureochrome1-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6868
Polymers14,7551
Non-polymers9317
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.563, 104.563, 68.010
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11B-523-

HOH

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Components

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Aureochrome1-like ... , 2 types, 2 molecules AB

#1: Protein Aureochrome1-like protein


Mass: 14382.223 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ochromonas danica (eukaryote) / Gene: OdAUREO1 / Production host: Escherichia coli (E. coli) / References: UniProt: C5NSW6
#2: Protein Aureochrome1-like protein


Mass: 14754.552 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ochromonas danica (eukaryote) / Gene: OdAUREO1 / Production host: Escherichia coli (E. coli) / References: UniProt: C5NSW6

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Non-polymers , 6 types, 140 molecules

#3: Chemical ChemComp-9O9 / 1-deoxy-1-(7,8-dimethyl-2,4-dioxo-3,4-dihydropyrimido[4,5-b]quinolin-10(2H)-yl)-5-O-phosphono-D-ribitol


Mass: 455.356 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H22N3O9P
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-ACT / ACETATE ION


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


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H2O

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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: 3.68 Å3/Da / Density % sol: 66.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Na citrate, 0.3 M NH4 chloride, 15-20% PEG 2000
PH range: 4.5 - 4.9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.97→90.55 Å / Num. obs: 30564 / % possible obs: 99.7 % / Redundancy: 11.1 % / Biso Wilson estimate: 27.4 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.07 / Rrim(I) all: 0.073 / Net I/σ(I): 18.2
Reflection shellResolution: 1.97→2.02 Å / Redundancy: 11.2 % / Rmerge(I) obs: 1.451 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2235 / CC1/2: 0.942 / Rrim(I) all: 1.521 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
xia2data reduction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5A8B

5a8b


Resolution: 2→90.55 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.951 / SU B: 10.242 / SU ML: 0.139 / Cross valid method: THROUGHOUT / ESU R: 0.134 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD 9 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2201 1501 5.1 %RANDOM
Rwork0.18746 ---
obs0.18917 27817 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.833 Å2
Baniso -1Baniso -2Baniso -3
1--2.37 Å2-1.19 Å20 Å2
2---2.37 Å20 Å2
3---7.7 Å2
Refinement stepCycle: 1 / Resolution: 2→90.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2042 0 108 127 2277
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.022204
X-RAY DIFFRACTIONr_bond_other_d0.0020.022027
X-RAY DIFFRACTIONr_angle_refined_deg1.7172.0142986
X-RAY DIFFRACTIONr_angle_other_deg1.00134707
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7735268
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.11124.851101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.40315358
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5291513
X-RAY DIFFRACTIONr_chiral_restr0.0960.2326
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022424
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02435
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5363.1351059
X-RAY DIFFRACTIONr_mcbond_other1.5153.1291056
X-RAY DIFFRACTIONr_mcangle_it2.4034.6831321
X-RAY DIFFRACTIONr_mcangle_other2.4034.6861322
X-RAY DIFFRACTIONr_scbond_it1.8763.4461145
X-RAY DIFFRACTIONr_scbond_other1.8763.4471146
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.025.031663
X-RAY DIFFRACTIONr_long_range_B_refined5.84637.1142665
X-RAY DIFFRACTIONr_long_range_B_other5.84637.1312666
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 121 -
Rwork0.349 2023 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.0898-0.2306-0.6324.59841.39122.1081-0.10960.407-0.2682-0.33720.21110.13130.1305-0.1662-0.10150.0597-0.0575-0.02020.0868-0.01490.0508-35.114534.5844-2.7867
23.20460.15650.49374.73161.11152.2727-0.0077-0.28680.42050.5425-0.04380.1676-0.0348-0.00220.05150.0928-0.02340.01690.043-0.03710.0613-46.769912.43963.7788
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A178 - 307
2X-RAY DIFFRACTION2B178 - 309

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