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- PDB-5mbj: Structure of a bacterial light-regulated adenylyl cyclase -

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Basic information

Entry
Database: PDB / ID: 5mbj
TitleStructure of a bacterial light-regulated adenylyl cyclase
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: 2.3 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)80,6533
Polymers80,1972
Non-polymers4561
Water1,47782
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7500 Å2
ΔGint-74 kcal/mol
Surface area29630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.660, 57.070, 71.310
Angle α, β, γ (deg.)82.420, 75.790, 76.880
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Beta subunit of photoactivated adenylyl cyclase


Mass: 40098.387 Da / Num. of mol.: 2 / Mutation: I8V/I116V
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


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


Mass: 18.015 Da / Num. of mol.: 82 / 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: 2.28 Å3/Da / Density % sol: 45.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: 0.1 M Tris-HCl pH 8.0, 0.3 M Mg(NO3)2, 23 % w/v PEG 2000; Cryoprotection in 0.1 M Tris HCl pH 8.0, 50 mM MgCl2, 35 % w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.954 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 10, 2016
RadiationMonochromator: DOUBLE-CRYSTAL Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.3→45.25 Å / Num. obs: 30125 / % possible obs: 95.9 % / Observed criterion σ(I): -3 / Redundancy: 1.8 % / Biso Wilson estimate: 46.51 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.059 / Rrim(I) all: 0.083 / Χ2: 0.937 / Net I/σ(I): 8.46 / Num. measured all: 53661
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.3-2.40.6981.096563374635900.440.98795.8
2.4-2.50.5121.55549320730640.6030.72495.5
2.5-2.60.4161.814584270225950.7310.58896
2.6-2.70.2972.433753231521800.8280.42194.2
2.7-30.1853.919009528650860.9260.26296.2
3-40.05910.4113981818178680.9920.08496.2
4-60.02821.637195421340650.9970.03996.5
6-100.02426.212360137613160.9980.03495.6
100.02134.096673873610.9980.0393.3

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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: 2.3→45.244 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 35.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2528 709 2.35 %
Rwork0.2032 29416 -
obs0.2045 30125 95.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 154.75 Å2 / Biso mean: 68.6337 Å2 / Biso min: 24.08 Å2
Refinement stepCycle: final / Resolution: 2.3→45.244 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5398 0 31 82 5511
Biso mean--94.38 53.25 -
Num. residues----675
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0155612
X-RAY DIFFRACTIONf_angle_d1.5397628
X-RAY DIFFRACTIONf_chiral_restr0.094912
X-RAY DIFFRACTIONf_plane_restr0.008953
X-RAY DIFFRACTIONf_dihedral_angle_d23.0722119
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3001-2.47770.3437970.30045902599996
2.4777-2.7270.3241170.28025863598095
2.727-3.12160.32611640.24375899606396
3.1216-3.93250.26841680.19885868603696
3.9325-45.2530.20481630.16335884604796
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)
13.4491-0.62240.16015.19381.48146.4545-0.2171-0.72560.50260.7720.07910.0954-0.6925-0.49950.08270.8057-0.01310.00190.6389-0.05940.4018-19.545616.988339.6125
23.26550.7110.08474.1558-0.85911.9162-0.05190.3043-0.0434-0.22860.17320.36770.0185-0.0814-0.10940.28230.0096-0.01310.2264-0.05720.3489-16.70116.81322.5992
33.7005-1.30541.20794.4329-1.936.27780.0755-0.6667-0.61810.29270.08910.11951.51040.6512-0.20941.03340.0103-0.07080.79790.0820.4617-10.35-7.235939.5274
43.56350.7112-0.09725.21870.42631.742-0.06280.33180.0456-0.30780.0755-0.05560.01440.0094-0.0120.27450.0260.00410.23230.06310.2601-16.7428-7.85272.3956
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
3X-RAY DIFFRACTION3chain 'B' and (resid 2 through 126 )B2 - 126
4X-RAY DIFFRACTION4chain 'B' and (resid 127 through 347 )B127 - 347

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