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- PDB-6i22: Flavin Analogue Sheds Light on Light-Oxygen-Voltage Domain Mechanism -

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Basic information

Entry
Database: PDB / ID: 6i22
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 / 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
FLAVIN MONONUCLEOTIDE / Aureochrome1-like protein
Similarity search - Component
Biological speciesOchromonas danica (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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
C: Aureochrome1-like protein
D: Aureochrome1-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,3608
Polymers59,5354
Non-polymers1,8254
Water9,548530
1
A: Aureochrome1-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3402
Polymers14,8841
Non-polymers4561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Aureochrome1-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3402
Polymers14,8841
Non-polymers4561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Aureochrome1-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3402
Polymers14,8841
Non-polymers4561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Aureochrome1-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3402
Polymers14,8841
Non-polymers4561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)150.180, 91.510, 99.840
Angle α, β, γ (deg.)90.00, 131.34, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-536-

HOH

21D-501-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAGLUGLUAA179 - 3112 - 134
21ALAALAGLUGLUBB179 - 3112 - 134
12ALAALAASNASNAA179 - 3102 - 133
22ALAALAASNASNCC179 - 3102 - 133
13ALAALAASNASNAA179 - 3102 - 133
23ALAALAASNASNDD179 - 3102 - 133
14ALAALAASNASNBB179 - 3102 - 133
24ALAALAASNASNCC179 - 3102 - 133
15ALAALAASNASNBB179 - 3102 - 133
25ALAALAASNASNDD179 - 3102 - 133
16GLYGLYGLUGLUCC178 - 3111 - 134
26GLYGLYGLUGLUDD178 - 3111 - 134

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Aureochrome1-like protein


Mass: 14883.666 Da / Num. of mol.: 4
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: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 530 / 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: 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: I04-1 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.66→71.05 Å / Num. obs: 117045 / % possible obs: 98 % / Redundancy: 6.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.083 / Rrim(I) all: 0.089 / Net I/σ(I): 12
Reflection shellResolution: 1.66→1.7 Å / Redundancy: 3.7 % / Rmerge(I) obs: 1.029 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 8720 / CC1/2: 0.543 / Rrim(I) all: 1.201 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
xia2data reduction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5A8B

5a8b


Resolution: 1.66→71.05 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.958 / SU B: 4.528 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.221 5747 4.9 %RANDOM
Rwork0.20303 ---
obs0.20389 111245 97.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.452 Å2
Baniso -1Baniso -2Baniso -3
1--0.34 Å2-0 Å2-0.03 Å2
2--1.49 Å2-0 Å2
3----0.44 Å2
Refinement stepCycle: 1 / Resolution: 1.66→71.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4180 0 124 530 4834
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0134467
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174043
X-RAY DIFFRACTIONr_angle_refined_deg1.661.696091
X-RAY DIFFRACTIONr_angle_other_deg1.4211.6019413
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4715556
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.81423.554242
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.25715743
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4341526
X-RAY DIFFRACTIONr_chiral_restr0.0850.2563
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025033
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02909
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_it1.4312.3772170
X-RAY DIFFRACTIONr_mcbond_other1.4312.3742169
X-RAY DIFFRACTIONr_mcangle_it2.2933.5442717
X-RAY DIFFRACTIONr_mcangle_other2.2933.5472718
X-RAY DIFFRACTIONr_scbond_it2.1012.7362297
X-RAY DIFFRACTIONr_scbond_other2.1012.7362296
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3273.9723366
X-RAY DIFFRACTIONr_long_range_B_refined6.90229.7015560
X-RAY DIFFRACTIONr_long_range_B_other6.90229.6995561
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A41910.1
12B41910.1
21A38610.14
22C38610.14
31A38640.14
32D38640.14
41B38820.13
42C38820.13
51B38800.13
52D38800.13
61C42640.08
62D42640.08
LS refinement shellResolution: 1.66→1.703 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 453 -
Rwork0.354 8264 -
obs--99.31 %
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)
12.55471.10470.41862.55860.09433.7380.05160.1094-0.2924-0.05640-0.04660.3878-0.1004-0.05160.0471-0.0241-0.00790.0645-0.01810.036832.3523-1.977725.5966
23.72350.4030.23682.89130.9642.5555-0.0617-0.08720.4853-0.0559-0.0358-0.0368-0.26950.13020.09740.0313-0.0237-0.01510.0671-0.01660.072912.95551.25488.2688
31.98640.581-0.03282.22580.15163.53770.03880.14790.2277-0.0952-0.03260.0896-0.4211-0.0138-0.00630.05960.0050.00820.03070.01890.031745.290626.968323.7074
43.6464-0.1147-0.19192.0369-0.67272.0238-0.0248-0.0034-0.4249-0.0906-0.02960.07750.2229-0.13730.05440.0403-0.01870.01290.0295-0.00370.057161.89418.06554.9145
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A179 - 311
2X-RAY DIFFRACTION2B178 - 311
3X-RAY DIFFRACTION3C178 - 311
4X-RAY DIFFRACTION4D179 - 311

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