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- PDB-3ulf: The light state structure of the blue-light photoreceptor Aureoch... -

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Basic information

Entry
Database: PDB / ID: 3ulf
TitleThe light state 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 / 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 / PHOSPHATE ION / Aureochrome1
Similarity search - Component
Biological speciesVaucheria frigida (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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
DepositionNov 10, 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 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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)116,23914
Polymers113,3116
Non-polymers2,9288
Water1,35175
1
A: Aureochrome1
B: Aureochrome1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7785
Polymers37,7702
Non-polymers1,0083
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint-27 kcal/mol
Surface area12960 Å2
MethodPISA
2
C: Aureochrome1
D: Aureochrome1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6834
Polymers37,7702
Non-polymers9132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3200 Å2
ΔGint-19 kcal/mol
Surface area13710 Å2
MethodPISA
3
E: Aureochrome1
F: Aureochrome1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7785
Polymers37,7702
Non-polymers1,0083
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4280 Å2
ΔGint-29 kcal/mol
Surface area13100 Å2
MethodPISA
4


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17740 Å2
ΔGint-103 kcal/mol
Surface area33710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.980, 73.980, 176.180
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: 18885.207 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.: 75 / Source method: isolated from a natural source / Formula: H2O
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: 2.13 Å3/Da / Density % sol: 42.18 %
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: 2.9→50 Å / Num. all: 21113 / Num. obs: 21007 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.4 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 24
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 6 % / Rmerge(I) obs: 0.615 / Mean I/σ(I) obs: 2 / % possible all: 99

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.6.1_357)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→34.105 Å / SU ML: 0.4 / σ(F): 1.36 / Phase error: 29.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2641 1071 5.14 %
Rwork0.201 --
obs0.2043 20832 99.4 %
all-20958 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 81.284 Å2 / ksol: 0.342 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-12.2098 Å20 Å2-0 Å2
2--12.2098 Å20 Å2
3----24.4195 Å2
Refinement stepCycle: LAST / Resolution: 2.9→34.105 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6092 0 196 75 6363
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036415
X-RAY DIFFRACTIONf_angle_d0.7038734
X-RAY DIFFRACTIONf_dihedral_angle_d18.8642316
X-RAY DIFFRACTIONf_chiral_restr0.05983
X-RAY DIFFRACTIONf_plane_restr0.0021109
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.03190.35681350.2712435X-RAY DIFFRACTION99
3.0319-3.19170.291410.21912491X-RAY DIFFRACTION99
3.1917-3.39150.27911320.18892433X-RAY DIFFRACTION99
3.3915-3.6530.23411380.17412460X-RAY DIFFRACTION99
3.653-4.02010.26411470.17632458X-RAY DIFFRACTION100
4.0201-4.60070.26151350.16742478X-RAY DIFFRACTION100
4.6007-5.79170.21411230.17642495X-RAY DIFFRACTION100
5.7917-34.10750.26941200.22622511X-RAY DIFFRACTION99
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)
11.6111-2.0821.02322.9355-0.24543.51150.02280.0438-0.1177-0.0513-0.13490.049-0.0765-0.4670.11220.2453-0.1142-0.00340.4463-0.06350.3716.5456-16.183516.2898
22.61790.3257-0.99763.3012-0.39013.9104-0.03720.36410.091-0.3346-0.03630.0821-0.02740.10570.08620.18980.10560.01180.35550.03630.309-4.3361-10.20470.4937
31.71610.4438-0.12211.06590.14030.12550.6068-1.1281-0.18350.6545-0.91980.36010.1078-0.39080.20131.3547-0.29250.55671.2456-0.23291.3298-2.6119-42.800815.1247
41.0278-0.12550.11442.3642-0.13710.5625-0.62340.4648-0.1727-0.49960.31571.35910.09790.14320.26591.1436-0.24510.20581.25-0.48151.2935-5.6043-39.3381-13.7095
53.8746-2.45180.60162.0617-1.22422.6686-0.0381-0.1109-0.1885-0.12570.17420.07730.41030.0113-0.06210.3515-0.08840.04730.19770.02420.238520.8418-20.4364-16.0521
62.3558-0.10010.0582.83790.66873.6837-0.0072-0.3129-0.20310.3108-0.1123-0.1046-0.04450.0090.11350.4230.0993-0.04980.2852-0.03880.312926.7111-41.3547-0.2494
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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