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- PDB-8qfg: Cryogenic crystal structure of the Photoactivated Adenylate Cycla... -

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Basic information

Entry
Database: PDB / ID: 8qfg
TitleCryogenic crystal structure of the Photoactivated Adenylate Cyclase OaPAC after 5 seconds of blue light illumination
ComponentsFamily 3 adenylate cyclase
KeywordsLYASE / Photoreceptor / BLUF / Adenylate Cyclase / PAC
Function / homology
Function and homology information


cyclic nucleotide biosynthetic process / blue light photoreceptor activity / adenylate cyclase activity / FAD binding / cell projection / 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 / Adenylate and Guanylate cyclase catalytic domain / Adenylyl cyclase class-3/4/guanylyl cyclase / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsChretien, A. / Nagel, M.F. / Botha, S. / de Wijn, R. / Brings, L. / Doerner, K. / Han, H. / C.P.Koliyadu, J. / Letrun, R. / Round, A. ...Chretien, A. / Nagel, M.F. / Botha, S. / de Wijn, R. / Brings, L. / Doerner, K. / Han, H. / C.P.Koliyadu, J. / Letrun, R. / Round, A. / Sato, T. / 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
Revision 1.3Feb 19, 2025Group: Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_struct_assembly_gen / pdbx_struct_oper_list
Item: _pdbx_entry_details.has_protein_modification

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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
Water1,928107
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)52.511, 141.425, 104.732
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-594-

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.: 107 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.47 Å3/Da / Density % sol: 50.29 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 50% protein at 10 mg/mL : 50 mM TRIS/HCl pH 8.5, 50 mM sodium chloride, 5 mM ATP 50% crystallization buffer : 100 mM SPG buffer pH 7.0, 1.2 M disodium succinate, 100 mM guanidine ...Details: 50% protein at 10 mg/mL : 50 mM TRIS/HCl pH 8.5, 50 mM sodium chloride, 5 mM ATP 50% crystallization buffer : 100 mM SPG buffer pH 7.0, 1.2 M disodium succinate, 100 mM guanidine hydrochloride, 5 mM magnesium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 1, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.7→42.08 Å / Num. obs: 42861 / % possible obs: 99.2 % / Redundancy: 13.3 % / Biso Wilson estimate: 33.74 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.033 / Rpim(I) all: 0.014 / Rrim(I) all: 0.036 / Χ2: 0.99 / Net I/σ(I): 34.9
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 12 % / Rmerge(I) obs: 0.864 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 2140 / CC1/2: 0.939 / Rpim(I) all: 0.373 / Rrim(I) all: 0.944 / Χ2: 0.68 / % possible all: 95.7

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Processing

Software
NameVersionClassification
XDSdata reduction
PHENIX1.20.1_4487refinement
Coot0.9.8.7model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→42.08 Å / SU ML: 0.2096 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.3226
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2299 2122 4.97 %
Rwork0.2096 40592 -
obs0.2106 42714 98.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.53 Å2
Refinement stepCycle: LAST / Resolution: 1.7→42.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2560 0 64 107 2731
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01332721
X-RAY DIFFRACTIONf_angle_d1.11163704
X-RAY DIFFRACTIONf_chiral_restr0.0714428
X-RAY DIFFRACTIONf_plane_restr0.0118467
X-RAY DIFFRACTIONf_dihedral_angle_d7.8338379
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.740.32331360.29952559X-RAY DIFFRACTION95.33
1.74-1.780.33371350.27042658X-RAY DIFFRACTION98.17
1.78-1.830.32521540.26892643X-RAY DIFFRACTION98.07
1.83-1.890.28971350.26632699X-RAY DIFFRACTION98.47
1.89-1.950.2911640.25412641X-RAY DIFFRACTION98.63
1.95-2.020.29411440.22622690X-RAY DIFFRACTION98.81
2.02-2.10.26611410.22742709X-RAY DIFFRACTION98.82
2.1-2.190.2661340.21672653X-RAY DIFFRACTION97.96
2.19-2.310.23071390.22242699X-RAY DIFFRACTION99.2
2.31-2.450.25681230.2262736X-RAY DIFFRACTION99.27
2.45-2.640.2361310.22032744X-RAY DIFFRACTION99.38
2.64-2.910.21861330.21582770X-RAY DIFFRACTION99.79
2.91-3.330.22351440.21682729X-RAY DIFFRACTION98.66
3.33-4.190.21491460.19032800X-RAY DIFFRACTION99.9
4.19-42.080.21111630.19262862X-RAY DIFFRACTION98.82

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