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- PDB-8qfi: Room temperature crystal structure of the Photoactivated Adenylat... -

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Basic information

Entry
Database: PDB / ID: 8qfi
TitleRoom temperature crystal structure of the Photoactivated Adenylate Cyclase OaPAC after blue light excitation at 1.8 us delay
ComponentsFamily 3 adenylate cyclase
KeywordsLYASE / Photoreceptor / BLUF / Adenylate Cyclase / PAC
Function / homology
Function and homology information


blue light photoreceptor activity / cAMP biosynthetic process / adenylate cyclase activity / FAD binding / cell projection / intracellular signal transduction / ATP binding / metal ion binding
Similarity search - Function
Sensors of blue-light using FAD / BLUF domain profile. / BLUF domain / Sensors of blue-light using FAD / Acylphosphatase-like domain superfamily / Adenylyl- / guanylyl cyclase, catalytic domain / Adenylyl cyclase class-3/4/guanylyl cyclase / Adenylate and Guanylate cyclase catalytic domain / Guanylate cyclase domain profile. / Nucleotide cyclase
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / FLAVIN MONONUCLEOTIDE / Family 3 adenylate cyclase
Similarity search - Component
Biological speciesOscillatoria acuminata PCC 6304 (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsChretien, A. / Nagel, M.F. / Botha, S. / de Wijn, R. / Brings, L. / Doerner, K. / Han, H. / C.P.Koliyadu, J. / Letrun, R. / Sato, T. ...Chretien, A. / Nagel, M.F. / Botha, S. / de Wijn, R. / Brings, L. / Doerner, K. / Han, H. / C.P.Koliyadu, J. / Letrun, R. / Sato, T. / Round, A. / Schmidt, C. / Secareanu, R. / von Stetten, D. / Vakili, M. / Wrona, A. / Bean, R. / Mancuso, A. / Schulz, J. / R.Pearson, A. / Kottke, T. / Lorenzen, K. / Schubert, R.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Federal Ministry for Education and Research Germany
CitationJournal: J.Mol.Biol. / Year: 2024
Title: Light-induced Trp in /Met out Switching During BLUF Domain Activation in ATP-bound Photoactivatable Adenylate Cyclase OaPAC.
Authors: Chretien, A. / Nagel, M.F. / Botha, S. / de Wijn, R. / Brings, L. / Dorner, K. / Han, H. / Koliyadu, J.C.P. / Letrun, R. / Round, A. / Sato, T. / Schmidt, C. / Secareanu, R.C. / von Stetten, ...Authors: Chretien, A. / Nagel, M.F. / Botha, S. / de Wijn, R. / Brings, L. / Dorner, K. / Han, H. / Koliyadu, J.C.P. / Letrun, R. / Round, A. / Sato, T. / Schmidt, C. / Secareanu, R.C. / von Stetten, D. / Vakili, M. / Wrona, A. / Bean, R. / Mancuso, A. / Schulz, J. / Pearson, A.R. / Kottke, T. / Lorenzen, K. / Schubert, R.
History
DepositionSep 4, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 1, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 13, 2024Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Family 3 adenylate cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3055
Polymers39,2931
Non-polymers1,0124
Water2,324129
1
A: Family 3 adenylate cyclase
hetero molecules

A: Family 3 adenylate cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,61010
Polymers78,5862
Non-polymers2,0248
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1
Unit cell
Length a, b, c (Å)54.300, 145.800, 105.300
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-613-

HOH

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Components

#1: Protein Family 3 adenylate cyclase


Mass: 39292.848 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oscillatoria acuminata PCC 6304 (bacteria)
Gene: Oscil6304_3613 / Production host: Escherichia coli (E. coli) / References: UniProt: K9TLZ5
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.65 Å3/Da / Density % sol: 53.62 %
Crystal growTemperature: 277 K / Method: batch mode
Details: 45% protein at 12 mg/mL : 50 mM TRIS/HCl pH 8.5, 50 mM sodium chloride, 5 mM ATP 45% crystallization buffer : 100 mM SPG buffer pH 7.0, 1.2 M disodium succinate, 100 mM guanidine ...Details: 45% protein at 12 mg/mL : 50 mM TRIS/HCl pH 8.5, 50 mM sodium chloride, 5 mM ATP 45% crystallization buffer : 100 mM SPG buffer pH 7.0, 1.2 M disodium succinate, 100 mM guanidine hydrochloride, 5 mM magnesium chloride 10% seeds from crushed macrocrystals

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: European XFEL / Beamline: SPB/SFX / Wavelength: 1.3332 Å
DetectorType: AGIPD / Detector: PIXEL / Date: May 7, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3332 Å / Relative weight: 1
ReflectionResolution: 1.815→31.63 Å / Num. obs: 36898 / % possible obs: 99.61 % / Redundancy: 711 % / Biso Wilson estimate: 29.64 Å2 / CC1/2: 0.983 / CC star: 0.996 / R split: 0.132 / Net I/σ(I): 1.2
Reflection shellResolution: 1.815→1.88 Å / Redundancy: 428 % / Mean I/σ(I) obs: 0.6 / Num. unique obs: 3192 / CC1/2: 0.391 / CC star: 0.75 / R split: 1.711 / % possible all: 84.92
Serial crystallography sample deliveryMethod: injection

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Processing

Software
NameVersionClassification
CrystFEL0.10.1data reduction
Xtrapol81.2.0data scaling
PHENIX1.20.1_4487refinement
Coot0.9.8.7model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→31.63 Å / SU ML: 0.3806 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 42.2159
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3392 1668 5 %
Rwork0.3064 31687 -
obs0.3081 33355 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.65 Å2
Refinement stepCycle: LAST / Resolution: 1.9→31.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2572 0 64 129 2765
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01242952
X-RAY DIFFRACTIONf_angle_d0.88694059
X-RAY DIFFRACTIONf_chiral_restr0.0644465
X-RAY DIFFRACTIONf_plane_restr0.0084516
X-RAY DIFFRACTIONf_dihedral_angle_d6.8622431
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.960.45841370.42912609X-RAY DIFFRACTION99.85
1.96-2.020.46581370.45652592X-RAY DIFFRACTION99.93
2.02-2.090.52341360.47952605X-RAY DIFFRACTION99.82
2.09-2.170.4851370.45972611X-RAY DIFFRACTION99.93
2.17-2.270.50271380.47132607X-RAY DIFFRACTION99.71
2.27-2.390.47181380.4282612X-RAY DIFFRACTION99.93
2.39-2.540.4241370.36982617X-RAY DIFFRACTION100
2.54-2.740.3881390.3322640X-RAY DIFFRACTION100
2.74-3.020.39621390.31412655X-RAY DIFFRACTION99.96
3.02-3.450.29571410.25532658X-RAY DIFFRACTION100
3.45-4.340.2611410.22082684X-RAY DIFFRACTION100
4.35-31.630.24461480.25442797X-RAY DIFFRACTION99.97

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