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- PDB-6t73: New antiparallel dimer of aureochrome 1a LOV domain mutants from ... -

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Basic information

Entry
Database: PDB / ID: 6t73
TitleNew antiparallel dimer of aureochrome 1a LOV domain mutants from Phaeodactylum tricornutum
ComponentsPtaureo1a lov2 domain
KeywordsFLAVOPROTEIN / Photoreceptor / Interface
Function / homology
Function and homology information


nucleotide binding / nucleus
Similarity search - Function
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 ...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 / Ptaureo1a lov2 domain
Similarity search - Component
Biological speciesPhaeodactylum tricornutum (Diatom)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.435 Å
AuthorsEssen, L.O. / Hepp, S.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationES152/16-1; TA320/7-1 Germany
CitationJournal: J.Mol.Biol. / Year: 2020
Title: An Optogenetic Tool for Induced Protein Stabilization Based on the Phaeodactylum tricornutum Aureochrome 1a Light-Oxygen-Voltage Domain.
Authors: Hepp, S. / Trauth, J. / Hasenjager, S. / Bezold, F. / Essen, L.O. / Taxis, C.
History
DepositionOct 21, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2020Group: Database references / Category: citation / Item: _citation.title
Revision 1.2May 20, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ptaureo1a lov2 domain
B: Ptaureo1a lov2 domain
C: Ptaureo1a lov2 domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,5479
Polymers54,0723
Non-polymers1,4756
Water00
1
A: Ptaureo1a lov2 domain
B: Ptaureo1a lov2 domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0677
Polymers36,0482
Non-polymers1,0195
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4930 Å2
ΔGint-36 kcal/mol
Surface area12950 Å2
MethodPISA
2
C: Ptaureo1a lov2 domain
hetero molecules

C: Ptaureo1a lov2 domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9604
Polymers36,0482
Non-polymers9132
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z+1/21
Buried area4650 Å2
ΔGint-18 kcal/mol
Surface area12400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.374, 168.374, 95.711
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Ptaureo1a lov2 domain


Mass: 18023.873 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phaeodactylum tricornutum (Diatom) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A140UHJ0
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


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


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
Has ligand of interestN

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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: 3.62 Å3/Da / Density % sol: 66.04 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES pH 7.5, 0.8 M NaH2PO4, 0.8 M H2KPO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.435→48.605 Å / Num. obs: 11046 / % possible obs: 98.98 % / Redundancy: 2 % / Biso Wilson estimate: 107.25 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.04636 / Rpim(I) all: 0.04636 / Rrim(I) all: 0.06556 / Net I/σ(I): 8.36
Reflection shellResolution: 3.435→3.56 Å / Redundancy: 2 % / Rmerge(I) obs: 0.4975 / Mean I/σ(I) obs: 1.29 / Num. unique obs: 1047 / CC1/2: 0.595 / Rpim(I) all: 0.4975 / Rrim(I) all: 0.7035 / % possible all: 92.89

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIX1.16_3549phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5a8b

5a8b


Resolution: 3.435→48.605 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.6
RfactorNum. reflection% reflection
Rfree0.278 578 5.26 %
Rwork0.2491 --
obs0.2505 10998 98.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 157.06 Å2 / Biso mean: 115.4566 Å2 / Biso min: 88.13 Å2
Refinement stepCycle: final / Resolution: 3.435→48.605 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3136 0 96 0 3232
Biso mean--107.96 --
Num. residues----408
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.435-3.78020.33121410.3304245296
3.7802-4.32690.28741390.27752599100
4.3269-5.45020.27841460.23492610100
5.4502-48.6050.2591520.2244275999
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)
11.1283-0.70680.33680.4727-0.16770.110.3925-0.85-0.2622.4034-0.8362-1.06291.23120.61510.00471.3559-0.05070.07091.73290.03351.199119.052958.93468.8423
20.5363-0.5887-0.17610.8075-0.10030.51320.2299-0.6412-2.10220.214-0.517-1.6577-0.57190.52280.00771.0386-0.01410.38471.5706-0.16951.310517.200967.10421.9583
30.6659-0.6206-0.40881.0145-0.20380.9314-0.19491.3143-0.3927-0.03860.90840.00610.00880.16170.00031.0340.19290.23661.5074-0.00091.22829.338969.16071.6808
41.35370.14691.7960.1460.34062.41170.29291.3549-0.1759-0.4001-0.46940.5936-0.3538-0.8197-0.00041.2434-0.04170.13091.5624-0.00771.360611.171768.425-11.1175
52.38870.36340.77541.43641.98322.677-0.08620.19480.0278-1.2094-0.270.425-0.22540.0875-0.00081.3592-0.0090.29191.3290.03571.29818.28563.9495-12.8933
60.7357-0.0769-0.0050.1462-0.09750.049-0.94350.77540.3995-2.2420.31780.5252-0.3615-0.50830.00411.52570.01250.07851.889-0.05590.951723.401957.4951-14.3146
71.78050.78410.70550.66220.80471.0322-0.3722.5319-0.2062-1.20220.16361.6611-0.6394-0.75050.01231.14280.0680.22811.3216-0.09661.185829.848562.6331-7.2715
80.8849-0.17170.29350.61170.78161.2757-0.59020.7123-0.5501-0.03860.30890.1289-0.164-0.2685-00.99510.06950.20071.442-0.06571.240537.282459.3534-6.9592
91.1829-0.15141.28091.0278-0.09511.6231-0.0716-0.0903-0.73510.69740.109-0.03010.53260.35360.00011.14240.15680.12491.34660.06751.218235.240759.595.9312
101.3769-0.22960.2291.5606-2.17332.8098-0.2774-0.043-0.19940.2188-0.40210.56-0.0899-0.51300.87540.07210.24451.1275-0.0671.268226.761960.60386.9582
111.00110.31930.4440.09440.11240.19210.1520.2086-0.859-2.3898-0.27020.37381.1903-0.22840.00011.5422-0.09180.12331.7988-0.13091.02952.052361.975312.4115
121.23061.14850.52521.32870.90081.3472-0.1097-0.8209-0.54780.73780.7775-0.2617-0.50010.55650.00051.0507-0.16010.38261.3503-0.09391.503314.682168.371819.4679
132.0886-2.1-0.72111.99990.69860.21590.3495-1.5699-0.25170.7304-0.0245-0.7548-0.13611.07050.00091.067-0.01920.22281.6074-0.10631.394812.901568.155832.2373
141.3052-0.9484-0.29372.1053-2.0333.0580.1684-0.18680.08680.1408-0.4839-0.1057-0.5497-0.5698-0.00031.0124-0.11880.35781.2606-0.0891.33884.729866.230333.5252
151.39350.6204-0.34970.34990.00150.3546-0.45460.5981-0.1515-0.02870.55670.73710.44170.07530.00391.2326-0.08250.23031.3842-0.0051.29886.57969.024119.2952
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 235 through 246 )A235 - 246
2X-RAY DIFFRACTION2chain 'A' and (resid 247 through 256 )A247 - 256
3X-RAY DIFFRACTION3chain 'A' and (resid 257 through 281)A257 - 281
4X-RAY DIFFRACTION4chain 'A' and (resid 282 through 335 )A282 - 335
5X-RAY DIFFRACTION5chain 'A' and (resid 336 through 369 )A336 - 369
6X-RAY DIFFRACTION6chain 'B' and (resid 235 through 246 )B235 - 246
7X-RAY DIFFRACTION7chain 'B' and (resid 247 through 256 )B247 - 256
8X-RAY DIFFRACTION8chain 'B' and (resid 257 through 281 )B257 - 281
9X-RAY DIFFRACTION9chain 'B' and (resid 282 through 335 )B282 - 335
10X-RAY DIFFRACTION10chain 'B' and (resid 336 through 369 )B336 - 369
11X-RAY DIFFRACTION11chain 'C' and (resid 235 through 246 )C235 - 246
12X-RAY DIFFRACTION12chain 'C' and (resid 257 through 281 )C257 - 281
13X-RAY DIFFRACTION13chain 'C' and (resid 282 through 335 )C282 - 335
14X-RAY DIFFRACTION14chain 'C' and (resid 336 through 369 )C336 - 369
15X-RAY DIFFRACTION15chain 'C' and (resid 247 through 256 )C247 - 256

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