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- PDB-6i21: Flavin Analogue Sheds Light on Light-Oxygen-Voltage Domain Mechanism -

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Basic information

Entry
Database: PDB / ID: 6i21
TitleFlavin Analogue Sheds Light on Light-Oxygen-Voltage Domain Mechanism
ComponentsAureochrome1-like protein
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 / PAS domain / Basic-leucine zipper domain superfamily / 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 / PAS domain / Basic-leucine zipper domain superfamily / 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 / DI(HYDROXYETHYL)ETHER / Aureochrome1-like protein
Similarity search - Component
Biological speciesOchromonas danica (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 1.2Aug 21, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aureochrome1-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,70015
Polymers15,0131
Non-polymers1,68814
Water2,324129
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3210 Å2
ΔGint-17 kcal/mol
Surface area8070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.389, 106.389, 67.486
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-408-

MG

21A-507-

HOH

31A-625-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Aureochrome1-like protein


Mass: 15012.846 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, 143 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 10-25% PEG 2K or 3K, 100 mM Na Acetate or Na Citrate, pH 4.5 - 4.9 Protein conc 10 mg/ml

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.5→67.48 Å / Num. obs: 36515 / % possible obs: 100 % / Redundancy: 20.7 % / Biso Wilson estimate: 22.2 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.071 / Rrim(I) all: 0.074 / Net I/av σ(I): 18.2 / Net I/σ(I): 18.2
Reflection shellResolution: 1.5→1.54 Å / Redundancy: 21.3 % / Rmerge(I) obs: 2.595 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2637 / CC1/2: 0.644 / Rrim(I) all: 2.725 / % possible all: 100

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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: 1.5→67.48 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.97 / SU B: 3.686 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.065 / ESU R Free: 0.062 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20501 1886 5.2 %RANDOM
Rwork0.17304 ---
obs0.17476 34209 98.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 26.378 Å2
Baniso -1Baniso -2Baniso -3
1--0.39 Å2-0.19 Å20 Å2
2---0.39 Å20 Å2
3---1.25 Å2
Refinement stepCycle: 1 / Resolution: 1.5→67.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1057 0 110 129 1296
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.021231
X-RAY DIFFRACTIONr_bond_other_d0.0020.021122
X-RAY DIFFRACTIONr_angle_refined_deg2.0062.0461668
X-RAY DIFFRACTIONr_angle_other_deg1.0443.0012612
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0545147
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.59425.26357
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.79715195
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.495157
X-RAY DIFFRACTIONr_chiral_restr0.1410.2176
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021342
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02234
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_it1.8281.313564
X-RAY DIFFRACTIONr_mcbond_other1.8141.311563
X-RAY DIFFRACTIONr_mcangle_it2.3171.978712
X-RAY DIFFRACTIONr_mcangle_other2.3191.979713
X-RAY DIFFRACTIONr_scbond_it2.4371.71666
X-RAY DIFFRACTIONr_scbond_other2.4381.709665
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.72.424954
X-RAY DIFFRACTIONr_long_range_B_refined3.88417.8211582
X-RAY DIFFRACTIONr_long_range_B_other3.88317.8191583
X-RAY DIFFRACTIONr_rigid_bond_restr2.75432351
X-RAY DIFFRACTIONr_sphericity_free27.908580
X-RAY DIFFRACTIONr_sphericity_bonded8.61652385
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 128 -
Rwork0.313 2487 -
obs--99.32 %
Refinement TLS params.Method: refined / Origin x: 34.65 Å / Origin y: -34.5578 Å / Origin z: 7.8458 Å
111213212223313233
T0.0732 Å2-0.0364 Å2-0.0068 Å2-0.0914 Å20.0229 Å2--0.0116 Å2
L2.0908 °21.1951 °20.6484 °2-1.9877 °2-0.1778 °2--2.2232 °2
S-0.1129 Å °0.1876 Å °0.1398 Å °-0.216 Å °0.0839 Å °0.0441 Å °-0.0552 Å °-0.1509 Å °0.0291 Å °

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