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

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Basic information

Entry
Database: PDB / ID: 8qfj
TitleRoom temperature crystal structure of the Photoactivated Adenylate Cyclase OaPAC after blue light excitation at 2.3 us delay
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 / 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. / 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

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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
Water2,288127
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-625-

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.: 127 / 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: 37632 / % possible obs: 98.52 % / Redundancy: 936 % / Biso Wilson estimate: 30.5 Å2 / CC1/2: 0.988 / CC star: 0.997 / R split: 0.11 / Net I/σ(I): 1.3
Reflection shellResolution: 1.815→1.88 Å / Redundancy: 563 % / Mean I/σ(I) obs: 0.8 / Num. unique obs: 3250 / CC1/2: 0.448 / CC star: 0.787 / % possible all: 86.37
Serial crystallography sample deliveryMethod: injection

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Processing

Software
NameVersionClassification
CrystFEL0.10.1data reduction
Xtrapol81.2.0refinement
PHENIX1.20.1_4487refinement
Coot0.9.8.7model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→31.63 Å / SU ML: 0.497 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 44.578
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3546 1669 5.01 %
Rwork0.2966 31675 -
obs0.2995 33344 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.9 Å2
Refinement stepCycle: LAST / Resolution: 1.9→31.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2574 0 64 127 2765
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00292937
X-RAY DIFFRACTIONf_angle_d0.75094035
X-RAY DIFFRACTIONf_chiral_restr0.0545463
X-RAY DIFFRACTIONf_plane_restr0.0095512
X-RAY DIFFRACTIONf_dihedral_angle_d7.9138427
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.960.59671380.51032609X-RAY DIFFRACTION99.89
1.96-2.020.51531360.48992593X-RAY DIFFRACTION99.93
2.02-2.090.53631370.47692606X-RAY DIFFRACTION99.89
2.09-2.170.4561380.43152608X-RAY DIFFRACTION99.85
2.17-2.270.58261370.45582603X-RAY DIFFRACTION99.53
2.27-2.390.3931380.39932610X-RAY DIFFRACTION99.85
2.39-2.540.431370.3532616X-RAY DIFFRACTION99.96
2.54-2.740.38711390.32772640X-RAY DIFFRACTION100
2.74-3.020.421400.30562653X-RAY DIFFRACTION99.93
3.02-3.450.32341390.25352660X-RAY DIFFRACTION100
3.45-4.340.25561420.21412683X-RAY DIFFRACTION100
4.35-31.630.28161480.23342794X-RAY DIFFRACTION99.86
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)
10.8784813481450.0141803621191-0.07104106438681.99595015055-0.2570139573221.731421208350.201478345198-0.207284737936-0.00540380442765-0.0369826060091-0.007783780495570.1165496130470.115178037811-0.227493030503-0.001424180809320.601310972499-0.06435817258210.02705637894150.4910151019980.09207898858050.532495469515-4.92688437858-10.5820150016-9.90577095729
21.145988202880.4929681685290.383762479350.527920680683-0.1949680555491.13343947458-0.113165483785-0.291796499418-0.227265428822-0.05552328449970.2246917568660.09878835735120.374905919437-0.04385073905980.007091596804190.577627783759-0.001020857735410.00942318051270.3972514808670.02596298170550.4728055797720.550804760244-3.38565009749-24.1432261805
30.9744154019870.07419495243480.393530978011.059120146380.1807589855011.341584264120.0207412465515-0.03252591054970.03566970690510.09855117598250.008529258435540.01425719275250.0476667533008-0.08858015757688.65311547731E-60.302229815480.00249483728760.01253331084830.2983832728040.002630863962050.294560321812-1.9502758924127.1038483291-14.8253117845
40.6709703580730.643801745746-0.5071642802531.589315093890.3439554013561.991766083660.166760744755-0.083995488940.568370969849-0.449563996551-0.0155602802012-0.238920638848-0.391677939405-0.0426923968230.05570431138990.520305354310.02666292895540.1384891058030.3969764592320.0004609604572440.435272688092-9.4930345962740.8177055869-8.07720635001
Refinement TLS group

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

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11(chain A and resid 1:96)1 - 961 - 96
22(chain A and resid 97:142)97 - 14297 - 142
33(chain A and resid 143:302)143 - 302143 - 302
44(chain A and resid 303:330)303 - 330303 - 330

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