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- PDB-5mbd: Structure of a bacterial light-regulated adenylyl cylcase -

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Basic information

Entry
Database: PDB / ID: 5mbd
TitleStructure of a bacterial light-regulated adenylyl cylcase
ComponentsBeta subunit of photoactivated adenylyl cyclase
KeywordsLYASE / BLUF / adenylyl cyclase / photoreceptor / optogenetics
Function / homology
Function and homology information


cyclic nucleotide biosynthetic process / blue light photoreceptor activity / 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 / 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 / Beta subunit of photoactivated adenylyl cyclase
Similarity search - Component
Biological speciesBeggiatoa sp. PS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsLindner, R. / Hartmann, E. / Tarnawski, M. / Winkler, A. / Frey, D. / Reinstein, J. / Meinhart, A. / Schlichting, I.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationFOR1279 Germany
CitationJournal: J. Mol. Biol. / Year: 2017
Title: Photoactivation Mechanism of a Bacterial Light-Regulated Adenylyl Cyclase.
Authors: Lindner, R. / Hartmann, E. / Tarnawski, M. / Winkler, A. / Frey, D. / Reinstein, J. / Meinhart, A. / Schlichting, I.
History
DepositionNov 8, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 5, 2017Provider: repository / Type: Initial release
Revision 1.1May 3, 2017Group: Database references
Revision 2.0Jan 17, 2024Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Database references / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_initial_refinement_model / pdbx_nonpoly_scheme
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _pdbx_nonpoly_scheme.auth_seq_num

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta subunit of photoactivated adenylyl cyclase
B: Beta subunit of photoactivated adenylyl cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,2366
Polymers80,2532
Non-polymers9844
Water2,270126
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8760 Å2
ΔGint-102 kcal/mol
Surface area30070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.700, 56.710, 77.730
Angle α, β, γ (deg.)104.650, 103.860, 102.720
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Beta subunit of photoactivated adenylyl cyclase


Mass: 40126.441 Da / Num. of mol.: 2 / Fragment: Beggiatoa photoactivatable adenylyl cyclase bPAC
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Beggiatoa sp. PS (bacteria) / Gene: BGP_1043 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A7BT71
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O

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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: 2.35 Å3/Da / Density % sol: 47.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: 0.1 M Na-MES pH 6.5, 0.6 M NaCl, 20 % w/v PEG 3350; 0.3 mM alpha,beta-methylene-ATP in drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 8, 2011
RadiationMonochromator: DOUBLE-CRYSTAL Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→44.3 Å / Num. obs: 33433 / % possible obs: 96.3 % / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Biso Wilson estimate: 38.44 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 11.43
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.25-2.350.5073.28195.1
2.35-2.40.3964.04195.9
2.4-2.50.3594.88196.5
2.5-2.60.2885.59196.6
2.6-2.70.227.19196.4
2.7-30.1528.99197
3-40.06416.05196.7
4-50.0422.24195.4
5-60.04123.14196.3
6-100.03523.14195.5
100.02926.4197.5

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XSCALEdata scaling
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5M27

5m27


Resolution: 2.25→44.289 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 25.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2172 980 2.93 %
Rwork0.1895 32453 -
obs0.1903 33433 96.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 115.78 Å2 / Biso mean: 51.7839 Å2 / Biso min: 15.67 Å2
Refinement stepCycle: final / Resolution: 2.25→44.289 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5417 0 64 126 5607
Biso mean--77.36 46.56 -
Num. residues----678
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045596
X-RAY DIFFRACTIONf_angle_d0.6897587
X-RAY DIFFRACTIONf_chiral_restr0.044898
X-RAY DIFFRACTIONf_plane_restr0.004941
X-RAY DIFFRACTIONf_dihedral_angle_d15.5253385
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.25-2.36860.29661340.26014581471595
2.3686-2.5170.27031410.24164658479996
2.517-2.71130.29051400.2264621476197
2.7113-2.98410.25841400.21264699483997
2.9841-3.41580.23011430.19174654479797
3.4158-4.3030.20641390.16724591473096
4.303-44.29790.16791430.16684649479297
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)
10.5099-0.16180.44260.69030.08621.33850.13610.0973-0.1873-0.0943-0.0369-0.01590.2946-0.0576-00.36-0.0319-0.01370.2951-0.0330.1456-21.3571-19.2642-37.352
21.50140.5358-0.18570.8169-0.17810.04680.0991-0.2016-0.1350.0189-0.073-0.0607-0.0062-0.0096-00.15530.0053-0.01480.1591-0.01940.1794-15.574-17.99941.4219
30.353-0.1158-0.58710.46920.46761.37490.02720.01260.1258-0.21350.00530.0244-0.40970.315600.4611-0.0728-0.00760.47280.0770.1979-11.04774.4427-38.3686
41.36660.3970.08391.20550.3079-0.02070.0102-0.14230.19020.02030.00910.06070.0185-0.0005-00.14130.01620.01330.16020.02160.1751-17.74857.57061.7703
50.0045-0.0051-0.01660.014-0.0220.0436-0.3282-0.09570.15190.030.03390.26020.1369-0.1196-00.3076-0.0332-0.01360.3174-0.02240.2433-27.9258-9.9689-19.3115
60.03020.00320.01660.0172-0.01370.0274-0.14470.2187-0.055-0.03980.11260.03290.10440.0298-00.3225-0.01820.02380.32580.00360.2173-5.2602-2.2895-19.1377
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 126 )A2 - 126
2X-RAY DIFFRACTION2chain 'A' and (resid 147 through 347 )A147 - 347
3X-RAY DIFFRACTION3chain 'B' and (resid 2 through 126 )B2 - 126
4X-RAY DIFFRACTION4chain 'B' and (resid 147 through 347 )B147 - 347
5X-RAY DIFFRACTION5chain 'A' and (resid 127 through 146 )A127 - 146
6X-RAY DIFFRACTION6chain 'B' and (resid 127 through 146 )B127 - 146

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