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

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Basic information

Entry
Database: PDB / ID: 5mbb
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: 3.1 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization

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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
B: Beta subunit of photoactivated adenylyl cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,1664
Polymers80,2532
Non-polymers9132
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8360 Å2
ΔGint-78 kcal/mol
Surface area30180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.420, 96.690, 163.570
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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

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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: 2.83 Å3/Da / Density % sol: 56.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: 0.1 M Na-MES pH 6.5, 0.2 M Mg acetate, 20 % w/v PEG 3000, 3% w/v 1,6-diaminohexane

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 2, 2010
RadiationMonochromator: DOUBLE-CRYSTAL Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.1→49.4 Å / Num. obs: 17193 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 11.6 % / Biso Wilson estimate: 76.05 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.24 / Net I/σ(I): 10.77
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
3.1-3.21.4472.050.707199.7
3.2-3.31.152.410.751100
3.3-3.41.0983.370.8291100
3.4-3.70.6875.290.9281100
3.7-3.80.4537.670.9611100
3.8-3.90.4327.890.9631100
3.9-40.3529.60.9681100
4-50.18814.550.991199.9
5-60.16116.560.994199.9
6-100.11220.430.997199.9
100.06829.170.994199.1

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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: 3.1→49.371 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 24.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2335 860 5 %
Rwork0.1981 16323 -
obs0.1998 17183 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 231.52 Å2 / Biso mean: 79.6319 Å2 / Biso min: 32.15 Å2
Refinement stepCycle: final / Resolution: 3.1→49.371 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5419 0 62 0 5481
Biso mean--87.24 --
Num. residues----677
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025653
X-RAY DIFFRACTIONf_angle_d0.517681
X-RAY DIFFRACTIONf_chiral_restr0.04912
X-RAY DIFFRACTIONf_plane_restr0.002954
X-RAY DIFFRACTIONf_dihedral_angle_d15.3933447
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.1-3.29410.36891400.286826632803
3.2941-3.54840.3141410.264826742815
3.5484-3.90540.2581410.214426842825
3.9054-4.47020.22251420.176227032845
4.4702-5.63070.19811450.160127342879
5.6307-49.37680.19621510.191728653016
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)
11.7951.1640.1915.1697-0.96533.19120.0463-0.012-0.00250.38740.01830.53140.533-0.13230.0470.71840.01410.18820.43990.04470.6156-5.4859-22.091132.4232
24.8966-0.2834-0.10172.51850.06232.405-0.00030.41360.2437-0.138-0.01680.1136-0.0574-0.14450.03090.3286-0.04520.02470.5110.09130.4122-10.21956.17677.4246
32.24641.40860.71444.5035-0.49523.37920.2845-0.2562-0.16661.4270.1271-0.53290.17870.4443-0.36841.09250.1748-0.16840.57460.09950.643714.1869-10.858644.1005
43.74210.5492-0.63782.85280.22972.27460.0110.40120.1493-0.13510.1483-0.1969-0.09530.1752-0.15610.34720.0251-0.03270.46590.06420.458815.09668.704911.9638
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 146 )A1 - 146
2X-RAY DIFFRACTION2chain 'A' and (resid 147 through 347 )A147 - 347
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 126 )B1 - 126
4X-RAY DIFFRACTION4chain 'B' and (resid 127 through 347 )B127 - 347

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