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- PDB-3ue6: The dark structure of the blue-light photoreceptor Aureochrome1 LOV -

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Basic information

Entry
Database: PDB / ID: 3ue6
TitleThe dark structure of the blue-light photoreceptor Aureochrome1 LOV
ComponentsAureochrome1
KeywordsSIGNALING PROTEIN / PAS/LOV domain / FMN-binding blue-light photoreceptor
Function / homology
Function and homology information


DNA-binding transcription factor activity / nucleotide binding / identical protein 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 / PHOSPHATE ION / Aureochrome1
Similarity search - Component
Biological speciesVaucheria frigida (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsMitra, D. / Yang, X. / Moffat, K.
CitationJournal: Structure / Year: 2012
Title: Crystal structures of Aureochrome1 LOV suggest new design strategies for optogenetics.
Authors: Mitra, D. / Yang, X. / Moffat, K.
History
DepositionOct 28, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2013Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aureochrome1
B: Aureochrome1
C: Aureochrome1
D: Aureochrome1
E: Aureochrome1
F: Aureochrome1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,75814
Polymers110,8306
Non-polymers2,9288
Water1,22568
1
A: Aureochrome1
B: Aureochrome1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9515
Polymers36,9432
Non-polymers1,0083
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4180 Å2
ΔGint-26 kcal/mol
Surface area12830 Å2
MethodPISA
2
C: Aureochrome1
D: Aureochrome1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8564
Polymers36,9432
Non-polymers9132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-18 kcal/mol
Surface area12820 Å2
MethodPISA
3
E: Aureochrome1
F: Aureochrome1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9515
Polymers36,9432
Non-polymers1,0083
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4230 Å2
ΔGint-26 kcal/mol
Surface area12790 Å2
MethodPISA
4


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17090 Å2
ΔGint-91 kcal/mol
Surface area33180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.987, 73.987, 177.468
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein
Aureochrome1


Mass: 18471.734 Da / Num. of mol.: 6 / Fragment: UNP residues 176-337
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaucheria frigida (eukaryote) / Gene: AUREO1 / Production host: Escherichia coli (E. coli) / References: UniProt: A8QW55
#2: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 2.19 Å3/Da / Density % sol: 43.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 100 mM phosphate-citrate buffer (pH 4.2), 20% (w/v) PEG 8000, and 200 mM NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 18, 2011
RadiationMonochromator: Bent Ge(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. all: 24820 / Num. obs: 24720 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.3 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 34.1
Reflection shellResolution: 2.75→2.8 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.6.1_357refinement
REFMAC5.6.0116refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→33.088 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.944 / SU ML: 0.42 / σ(F): 1.38 / Phase error: 30.75 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflection
Rfree0.2563 1254 5.1 %
Rwork0.1923 --
obs0.1956 24612 99.64 %
all-23534 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.191 Å2 / ksol: 0.323 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-12.2009 Å20 Å2-0 Å2
2--12.2009 Å20 Å2
3----24.4019 Å2
Refinement stepCycle: LAST / Resolution: 2.75→33.088 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6128 0 196 68 6392
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046437
X-RAY DIFFRACTIONf_angle_d0.7638769
X-RAY DIFFRACTIONf_dihedral_angle_d19.0112329
X-RAY DIFFRACTIONf_chiral_restr0.052987
X-RAY DIFFRACTIONf_plane_restr0.0021113
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7501-2.86020.37181400.27812575X-RAY DIFFRACTION99
2.8602-2.99030.31871370.25022579X-RAY DIFFRACTION100
2.9903-3.14780.31431450.24312575X-RAY DIFFRACTION100
3.1478-3.34490.31541450.232613X-RAY DIFFRACTION100
3.3449-3.60280.24621210.19682614X-RAY DIFFRACTION100
3.6028-3.96480.25411380.18022600X-RAY DIFFRACTION100
3.9648-4.53730.22861680.17082572X-RAY DIFFRACTION100
4.5373-5.71180.24181280.16212637X-RAY DIFFRACTION100
5.7118-33.09040.22141320.17842593X-RAY DIFFRACTION98
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)
13.7588-1.77221.45874.0221-0.41883.46210.0888-0.0059-0.2046-0.1722-0.04140.18090.0141-0.1859-0.00010.5325-0.08820.02980.5929-0.07850.528416.0875-16.221416.2779
22.8670.51770.07143.8824-0.96355.2879-0.01890.38910.0791-0.44390.04170.0515-0.1055-0.19790.00010.47160.08760.04680.6238-0.00580.6211-4.6863-10.11350.7504
33.5548-0.27631.1773.43380.50292.14890.1367-0.5886-0.37960.7074-0.34490.37630.3987-0.4427-0.00021.0672-0.1920.25590.8682-0.02550.9939-3.1334-42.945914.3557
42.72510.883-0.61844.37-2.03081.2992-0.3180.3666-0.037-0.58340.33880.450.4541-0.371500.9504-0.17230.04441.0413-0.23421.0285-5.6222-39.7244-13.1597
53.7327-1.3763-0.02733.385-1.86522.9595-0.0815-0.2917-0.20670.03310.13220.27330.1405-0.0968-0.00010.6316-0.03990.09930.5565-0.03020.548520.549-21.2625-15.491
63.56320.52160.49853.1197-0.13765.11830.0823-0.3751-0.00880.3974-0.0991-0.04180.23170.2569-0.00010.61670.1040.02270.4921-0.04820.617926.8704-41.7158-0.6259
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D
5X-RAY DIFFRACTION5chain E
6X-RAY DIFFRACTION6chain F

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