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

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Basic information

Entry
Database: PDB / ID: 5nby
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
FLAVIN MONONUCLEOTIDE / Beta subunit of photoactivated adenylyl cyclase
Similarity search - Component
Biological speciesBeggiatoa sp. PS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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
DepositionMar 2, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 5, 2017Provider: repository / Type: Initial release
Revision 1.1May 3, 2017Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)40,5672
Polymers40,1101
Non-polymers4561
Water30617
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)81,1344
Polymers80,2212
Non-polymers9132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area8480 Å2
ΔGint-74 kcal/mol
Surface area30260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.430, 143.300, 57.280
Angle α, β, γ (deg.)90.000, 135.480, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-508-

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-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.4549.89
2
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7 / Details: 0.1 M Na-HEPES pH 7.0, 20 % w/v PEG 3350

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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: 2.5→45.501 Å / Num. obs: 13360 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 10.106 % / Biso Wilson estimate: 59.78 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.151 / Rrim(I) all: 0.159 / Χ2: 0.963 / Net I/σ(I): 13.65 / Num. measured all: 135017 / Scaling rejects: 548
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.5-2.610.3251.0192.4914690.8071.07299
2.6-2.710.1560.753.2612740.8890.7998.8
2.7-310.0980.4435.1928540.9540.46798.8
3-410.0930.19113.0544670.9920.20198.6
4-610.0830.1228.6223050.9920.12698.3
6-109.9590.10234.187760.9980.10797
10-45.5019.4560.11141.612150.9870.11893.9

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXdev_2645refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5M27

5m27


Resolution: 2.5→45.501 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 33.22
RfactorNum. reflection% reflection
Rfree0.2564 670 5.02 %
Rwork0.1912 --
obs0.1945 13356 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 162.75 Å2 / Biso mean: 74.7747 Å2 / Biso min: 38.7 Å2
Refinement stepCycle: final / Resolution: 2.5→45.501 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2690 0 31 17 2738
Biso mean--91.68 60 -
Num. residues----337
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082774
X-RAY DIFFRACTIONf_angle_d0.9543759
X-RAY DIFFRACTIONf_chiral_restr0.052445
X-RAY DIFFRACTIONf_plane_restr0.005468
X-RAY DIFFRACTIONf_dihedral_angle_d15.431680
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.5001-2.69310.42711330.307925102643
2.6931-2.96410.31841400.26325292669
2.9641-3.39290.3061320.229225362668
3.3929-4.27410.25641340.181225412675
4.2741-45.50810.20191310.155525702701
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)
15.16741.4246-0.42994.61221.39242.90260.1061-0.3306-0.2470.2876-0.09590.72670.2751-0.2122-0.02230.8331-0.04580.04730.40760.05450.56421.4404-38.90061.307
22.0917-1.04290.00191.4359-0.11952.51810.0406-0.15740.0115-0.0258-0.0257-0.09480.07520.072-0.01070.4307-0.0798-0.01480.42650.04240.356425.4397-5.29925.3082
37.6548-0.5643.19354.90660.21396.7075-0.0914-0.65130.85220.1126-0.1959-0.0953-0.8228-0.25110.33610.46270.04070.04610.4325-0.04440.517619.01169.8028.4662
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 285 )A127 - 285
3X-RAY DIFFRACTION3chain 'A' and (resid 286 through 347 )A286 - 347

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