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

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Basic information

Entry
Database: PDB / ID: 5mbe
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: 2.4 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 / 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
Water1,964109
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8390 Å2
ΔGint-77 kcal/mol
Surface area30020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.480, 56.310, 77.450
Angle α, β, γ (deg.)105.790, 103.670, 102.700
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 / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2.3 Å3/Da / Density % sol: 46.48 %
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: 2.4→44.1 Å / Num. obs: 27155 / % possible obs: 96.9 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 43.63 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 11.34
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.4-2.50.5223.18196.2
2.5-2.60.4113.99196.8
2.6-2.70.315.04197.1
2.7-30.1997.08197.4
3-40.08314197.2
4-50.0520.73195.8
5-60.04921.42197.1
6-100.04122.41196.3
100.03126.94196.9

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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: 2.4→44.082 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 24.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2311 796 2.93 %
Rwork0.1963 26358 -
obs0.1974 27154 97.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 183.68 Å2 / Biso mean: 69.0605 Å2 / Biso min: 21.48 Å2
Refinement stepCycle: final / Resolution: 2.4→44.082 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5403 0 62 109 5574
Biso mean--99.79 50.96 -
Num. residues----676
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025593
X-RAY DIFFRACTIONf_angle_d0.4377588
X-RAY DIFFRACTIONf_chiral_restr0.039899
X-RAY DIFFRACTIONf_plane_restr0.003942
X-RAY DIFFRACTIONf_dihedral_angle_d12.8783386
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.55040.28821350.25764380451596
2.5504-2.74730.2831330.23134397453097
2.7473-3.02370.29281340.21834418455298
3.0237-3.46110.20191320.19524413454598
3.4611-4.360.23531290.17834367449696
4.36-44.08990.20231330.18474383451697
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)
13.33070.15332.25713.7360.70455.96620.19950.5191-0.3931-0.5702-0.05190.02751.0289-0.4061-0.12820.8549-0.1237-0.05170.854-0.02950.4049-21.0618-18.8377-37.5869
24.20330.1588-0.30223.2382-0.2991.51350.0497-0.4011-0.17390.2252-0.0377-0.02150.01050.0161-0.04230.2779-0.0019-0.0060.236-0.07080.3709-16.4739-17.653-0.7672
32.320.8661-2.90034.0548-0.30853.9276-0.08820.23410.2176-0.62740.10350.2504-1.30220.953-0.07610.9919-0.1849-0.0411.13030.18690.48-11.21535.1487-38.005
44.8318-0.3139-0.05563.7810.53841.5193-0.0433-0.35750.19650.27230.07530.1144-0.0384-0.0613-0.0420.3086-0.00690.00230.24360.07290.3198-16.39146.192-0.6015
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 3 through 126 )B3 - 126
4X-RAY DIFFRACTION4chain 'B' and (resid 127 through 347 )B127 - 347

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