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- PDB-6i25: Flavin Analogue Sheds Light on Light-Oxygen-Voltage Domain Mechanism -

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Basic information

Entry
Database: PDB / ID: 6i25
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 / nucleus / metal ion binding
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-5DD / Chem-9O9 / Aureochrome1-like protein
Similarity search - Component
Biological speciesOchromonas danica (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsRizkallah, P.J. / Kalvaitis, M.E.
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 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jan 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 / struct_conn_type
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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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 / _struct_conn_type.id
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aureochrome1-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9855
Polymers15,0131
Non-polymers9724
Water2,720151
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint-17 kcal/mol
Surface area7550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.287, 106.287, 67.859
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-402-

MG

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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 , 5 types, 155 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-5DD / [(2~{R},3~{S},4~{S})-5-[(4~{a}~{R})-7,8-dimethyl-2,4-bis(oxidanylidene)-4~{a},5-dihydropyrimido[4,5-b]quinolin-10-yl]-2,3,4-tris(oxidanyl)pentyl] dihydrogen phosphate


Mass: 457.372 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H24N3O9P
#5: 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.: 1 / Source method: obtained synthetically / Formula: C18H22N3O9P
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 3.69 Å3/Da / Density % sol: 66.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1.5-3 M Na malonate, 0.1 M Tris.acetate / PH range: 7.5 - 8.0

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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 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: 1.97→54.62 Å / Num. obs: 16503 / % possible obs: 100 % / Redundancy: 20.9 % / Biso Wilson estimate: 17.5 Å2 / Net I/σ(I): 7.9
Reflection shellResolution: 1.97→2.02 Å

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Processing

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

5a8b


Resolution: 1.97→54.62 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.928 / SU B: 10.291 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.203 / ESU R Free: 0.128 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2223 674 4.1 %RANDOM
Rwork0.17692 ---
obs0.17901 15792 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 23.889 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å2-0.04 Å20 Å2
2---0.07 Å20 Å2
3---0.24 Å2
Refinement stepCycle: 1 / Resolution: 1.97→54.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1057 0 64 151 1272
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.021187
X-RAY DIFFRACTIONr_bond_other_d0.0020.021065
X-RAY DIFFRACTIONr_angle_refined_deg1.6972.0351632
X-RAY DIFFRACTIONr_angle_other_deg1.0293.0012486
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4095147
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.39725.53656
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.65915195
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.279156
X-RAY DIFFRACTIONr_chiral_restr0.1160.2177
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021330
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02229
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_it1.4181.382559
X-RAY DIFFRACTIONr_mcbond_other1.4121.382558
X-RAY DIFFRACTIONr_mcangle_it1.8822.068703
X-RAY DIFFRACTIONr_mcangle_other1.8842.069704
X-RAY DIFFRACTIONr_scbond_it1.581.613626
X-RAY DIFFRACTIONr_scbond_other1.581.613627
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.0322.373925
X-RAY DIFFRACTIONr_long_range_B_refined3.5117.5751478
X-RAY DIFFRACTIONr_long_range_B_other3.5117.5721479
X-RAY DIFFRACTIONr_rigid_bond_restr1.76532248
X-RAY DIFFRACTIONr_sphericity_free28.691585
X-RAY DIFFRACTIONr_sphericity_bonded6.67552291
LS refinement shellResolution: 1.97→2.021 Å
RfactorNum. reflection% reflection
Rwork0.254 1177 -
Rfree-0 -
obs--99.83 %
Refinement TLS params.Method: refined / Origin x: -34.6368 Å / Origin y: 34.5412 Å / Origin z: 7.9457 Å
111213212223313233
T0.0491 Å20.0034 Å2-0.0107 Å2-0.0563 Å2-0.0173 Å2--0.0093 Å2
L1.9291 °20.8559 °2-0.8806 °2-2.1116 °20.0369 °2--1.5811 °2
S-0.0474 Å °0.1979 Å °-0.0962 Å °-0.2249 Å °0.028 Å °0.0273 Å °0.1085 Å °0.0007 Å °0.0194 Å °

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