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

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Basic information

Entry
Database: PDB / ID: 8qfe
TitleCryogenic crystal structure of the Photoactivated Adenylate Cyclase OaPAC
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 / ATP binding / metal ion binding
Similarity search - Function
: / BLUF domain profile. / BLUF domain / Sensors of blue-light using FAD / 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
FLAVIN MONONUCLEOTIDE / Family 3 adenylate cyclase
Similarity search - Component
Biological speciesOscillatoria acuminata PCC 6304 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsChretien, A. / Nagel, M.F. / Botha, S. / de Wijn, R. / Brings, L. / Doerner, K. / Han, H. / Koliyadu, J. / Letrun, R. / Round, A. ...Chretien, A. / Nagel, M.F. / Botha, S. / de Wijn, R. / Brings, L. / Doerner, K. / Han, H. / 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. / 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

Downloads & links

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Assembly

Deposited unit
A: Family 3 adenylate cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7733
Polymers39,2931
Non-polymers4812
Water5,909328
1
A: Family 3 adenylate cyclase
hetero molecules
x 5
A: Family 3 adenylate cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)238,64118
Polymers235,7576
Non-polymers2,88412
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
Unit cell
Length a, b, c (Å)52.856, 146.202, 103.595
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-690-

HOH

21A-700-

HOH

31A-767-

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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 328 / 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: 2.47 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: ESRF / Beamline: ID23-2 / Wavelength: 0.8731 Å
DetectorType: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Feb 23, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8731 Å / Relative weight: 1
ReflectionResolution: 1.5→33.86 Å / Num. obs: 64596 / % possible obs: 100 % / Redundancy: 13 % / Biso Wilson estimate: 21.64 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.021 / Rrim(I) all: 0.055 / Χ2: 1.04 / Net I/σ(I): 25
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 12.8 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 3212 / CC1/2: 0.846 / Χ2: 0.8 / % possible all: 100

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Processing

Software
NameVersionClassification
MxCuBEdata collection
XDSdata reduction
PHENIX1.20.1_4487refinement
Coot0.9.8.7model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→31.22 Å / SU ML: 0.1539 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.8807
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1887 3164 4.9 %
Rwork0.1643 61379 -
obs0.1655 64543 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.5 Å2
Refinement stepCycle: LAST / Resolution: 1.5→31.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2712 0 32 328 3072
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01283214
X-RAY DIFFRACTIONf_angle_d1.18564415
X-RAY DIFFRACTIONf_chiral_restr0.0688499
X-RAY DIFFRACTIONf_plane_restr0.0122590
X-RAY DIFFRACTIONf_dihedral_angle_d5.6817477
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.520.2911390.26032636X-RAY DIFFRACTION99.96
1.52-1.550.30531480.24182630X-RAY DIFFRACTION99.93
1.55-1.570.28331130.22632647X-RAY DIFFRACTION100
1.57-1.60.26151140.21492664X-RAY DIFFRACTION100
1.6-1.630.23471160.20322663X-RAY DIFFRACTION100
1.63-1.660.24211330.19972676X-RAY DIFFRACTION99.96
1.66-1.690.2291450.20552599X-RAY DIFFRACTION99.96
1.69-1.730.26711350.20692662X-RAY DIFFRACTION100
1.73-1.770.23361410.18992646X-RAY DIFFRACTION99.96
1.77-1.810.24111250.17612651X-RAY DIFFRACTION99.89
1.81-1.860.20271540.17292608X-RAY DIFFRACTION100
1.86-1.920.20851270.15842671X-RAY DIFFRACTION99.96
1.92-1.980.1821450.162652X-RAY DIFFRACTION99.96
1.98-2.050.22081640.17332643X-RAY DIFFRACTION99.96
2.05-2.130.1921200.16642662X-RAY DIFFRACTION100
2.13-2.230.18761620.14592656X-RAY DIFFRACTION100
2.23-2.350.181210.14582693X-RAY DIFFRACTION100
2.35-2.490.17711350.15492679X-RAY DIFFRACTION100
2.49-2.690.17521330.14922684X-RAY DIFFRACTION100
2.69-2.960.1631620.15852676X-RAY DIFFRACTION99.96
2.96-3.380.19751310.15932721X-RAY DIFFRACTION100
3.38-4.260.12741370.1422728X-RAY DIFFRACTION100
4.26-31.220.20611640.17562832X-RAY DIFFRACTION99.57
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)
10.381565221238-0.1381342035670.06487041858671.3812567356-0.9616532652281.394760736690.00905708409263-0.0951177693921-0.0520810414588-0.05076752553980.07607311050220.1029418106830.219544347957-0.0605947582485-0.08098545777210.322380176374-0.0250296921007-0.01004674525160.2597587686070.007064538308570.155711599846-3.99897212165-7.65703681577-14.4981202866
20.451724540043-0.0286008835469-0.003802478968351.110350052440.4930898745091.438483841530.051036263679-0.03332604080810.109644805950.0459467303998-0.01196362572520.0108953794083-0.134126694401-0.0495489264919-0.02653637263460.2196405732190.005197450876210.01082640947920.2178390537360.002875256375630.12495952205-2.7618210852928.8607456232-14.1266979307
30.6201665687740.0901304699827-2.305048184917.890745898-0.09015519042828.59143538085-0.0597413955295-0.008908292033331.00466313759-0.2179412847630.148458916470.0245546026913-1.66757762348-0.28375379865-0.002800890553940.913047759818-0.156051051471-0.1226193095910.753580861247-0.1242425963590.75943149322812.821018395538.5366649686-7.10048428641
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 146 )1 - 1461 - 146
22chain 'A' and (resid 147 through 327 )147 - 327147 - 327
33chain 'A' and (resid 328 through 350 )328 - 350328 - 350

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