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

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Basic information

Entry
Database: PDB / ID: 5mbk
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 / 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 / Beta subunit of photoactivated adenylyl cyclase
Similarity search - Component
Biological speciesBeggiatoa sp. PS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 1.2Jan 17, 2024Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)40,6664
Polymers40,1101
Non-polymers5563
Water1,18966
1
A: Beta subunit of photoactivated adenylyl cyclase
hetero molecules

A: Beta subunit of photoactivated adenylyl cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,3328
Polymers80,2212
Non-polymers1,1126
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area8890 Å2
ΔGint-113 kcal/mol
Surface area30150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.600, 143.360, 57.480
Angle α, β, γ (deg.)90.000, 135.910, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-562-

HOH

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Components

#1: Protein Beta subunit of photoactivated adenylyl cyclase


Mass: 40110.441 Da / Num. of mol.: 1 / Fragment: Beggiatoa photoactivatable adenylyl cyclase bPAC / Mutation: Y7F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Beggiatoa sp. PS (bacteria) / Gene: BGP_1043 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A7BT71
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


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


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 2.49 Å3/Da / Density % sol: 50.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: 0.1 M Na-HEPES pH 7.0, 20 % w/v PEG 3350; soak in 50mM Tris-HCl pH 7.6, 115 mM MgCl2, 48 mM ATP, 35% (w/v) PEG 3350 before cryo-cooling

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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: Nov 20, 2015
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: 2.3→45.9 Å / Num. obs: 17359 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 5.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.103 / Net I/σ(I): 10.29
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
2.3-2.40.9831.840.682198.7
2.4-2.50.6962.580.794198.8
2.5-30.3454.790.943199
3-40.09913.280.994198.5
4-60.05224.190.996198.4
6-100.05125.060.997196
100.04731.850.997194.3

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Processing

Software
NameVersionClassification
PHENIXdev_2196refinement
XSCALEdata scaling
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5M27

5m27


Resolution: 2.4→45.88 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 30.34
RfactorNum. reflection% reflection
Rfree0.2638 758 4.96 %
Rwork0.2089 --
obs0.2117 15281 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 169.67 Å2 / Biso mean: 63.5584 Å2 / Biso min: 20.5 Å2
Refinement stepCycle: final / Resolution: 2.4→45.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2710 0 33 66 2809
Biso mean--53.42 52.06 -
Num. residues----339
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132785
X-RAY DIFFRACTIONf_angle_d1.3573772
X-RAY DIFFRACTIONf_chiral_restr0.071448
X-RAY DIFFRACTIONf_plane_restr0.007466
X-RAY DIFFRACTIONf_dihedral_angle_d17.8251683
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.4-2.58530.33931490.27428933042
2.5853-2.84540.3011590.241528823041
2.8454-3.25710.29331460.228829093055
3.2571-4.10320.25051550.199929133068
4.1032-45.88820.23791490.187129263075
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)
11.38161.1791-0.34482.61550.26481.5869-0.0181-0.11680.13420.2262-0.10751.4490.1776-0.19590.04590.7928-0.07060.16840.3884-0.00520.925122.0627-39.41672.3786
21.8965-0.7115-0.00160.5471-0.34682.52010.0339-0.10030.03360.0147-0.0069-0.0158-0.067-0.0042-0.07220.2311-0.0348-0.00120.25180.02060.274423.9615-1.5686.1165
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 127 through 347 )A127 - 347

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