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

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Basic information

Entry
Database: PDB / ID: 5mbg
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 / Adenylyl cyclase class-3/4/guanylyl cyclase / Adenylate and Guanylate cyclase catalytic domain / Guanylate cyclase domain profile. / Nucleotide cyclase
Similarity search - Domain/homology
IODIDE ION / 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 / diffrn_radiation_wavelength / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9135
Polymers23,4051
Non-polymers5084
Water50428
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)47,82510
Polymers46,8102
Non-polymers1,0158
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z+1/21
Buried area4550 Å2
ΔGint-29 kcal/mol
Surface area16450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.720, 101.790, 80.270
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Beta subunit of photoactivated adenylyl cyclase


Mass: 23404.893 Da / Num. of mol.: 1 / Fragment: Adenylyl Cyclase Domain, residues 145-350 / Mutation: delta-144
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-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: I
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 2.21 Å3/Da / Density % sol: 44.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: 0.1 M Na-HEPES pH 7.0, 0.2 M NaI, 20 % w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 11, 2011
RadiationMonochromator: DOUBLE-CRYSTAL Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.3→45.397 Å / Num. obs: 9537 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 12.4 % / Biso Wilson estimate: 46.51 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.108 / Rrim(I) all: 0.112 / Χ2: 0.978 / Net I/σ(I): 17.42 / Num. measured all: 118071
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.3-2.41.0993.514080112311140.8721.14699.2
2.4-2.50.7954.64114129409370.9390.8399.7
2.5-2.70.5227.5817938151915130.9770.54599.6
2.7-30.32612.8221088158015790.9920.33999.9
3-40.10723.9431672248224820.9980.111100
4-50.06534.52107799149140.9980.068100
5-60.06535.346383953950.9980.068100
6-100.05534.8450834624620.9990.057100
100.04836.5213811421410.9990.05199.3

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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→45.397 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 41.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2925 474 4.97 %
Rwork0.2403 9061 -
obs0.2431 9535 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 149.48 Å2 / Biso mean: 63.5262 Å2 / Biso min: 22.71 Å2
Refinement stepCycle: final / Resolution: 2.3→45.397 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1501 0 4 28 1533
Biso mean--102 57.81 -
Num. residues----192
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0011528
X-RAY DIFFRACTIONf_angle_d0.3542068
X-RAY DIFFRACTIONf_chiral_restr0.038250
X-RAY DIFFRACTIONf_plane_restr0.003257
X-RAY DIFFRACTIONf_dihedral_angle_d13.368913
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.63270.41281550.31582938309399
2.6327-3.31680.33231560.271930013157100
3.3168-45.40530.25651630.214831223285100
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)
18.0975-3.6874.17656.4536-0.57216.7185-0.3583-1.9489-0.73030.19670.73660.09410.2260.6274-0.29480.46220.01470.140.6323-0.01640.2969-15.0354-20.161713.9628
22.00093.65296.82883.3922-0.35718.15740.3938-1.21930.2640.7299-0.5806-0.2676-1.998-2.17410.11950.60190.21420.07270.6152-0.01410.554-41.1507-12.384412.0039
38.82850.3182-1.58352.34672.48485.66950.19940.1784-0.5222-0.01280.02720.08360.1244-0.5789-0.19270.33610.00740.04170.14270.00070.2416-30.0039-23.83377.4263
43.9526-0.3840.21673.51140.09045.4916-0.07960.78020.0234-0.2304-0.12720.0997-0.0060.39060.25820.3323-0.03310.02350.24960.00570.2564-27.1187-17.56870.9067
55.6279-1.58781.20932.8001-1.07293.4939-0.15610.0762-0.33180.67960.4067-0.142-0.35271.098-0.20040.5722-0.03510.02810.406-0.0370.2661-14.0594-19.949115.9913
68.84646.835-7.90126.4147-5.13499.2029-0.5480.286-0.225-0.63651.23650.95611.5646-2.158-0.41470.9421-0.30150.00280.97980.18780.6827-18.4838-28.017326.2164
74.3327-3.82174.09118.5499-5.34297.4841-1.0848-2.04431.4651.9320.761-0.1122-1.7028-1.4520.28440.62150.0283-0.03070.3423-0.150.3274-20.4718-9.053814.1266
85.5042-0.12841.43923.9154-2.69728.36230.10710.57970.814-0.7044-0.1703-1.4267-0.04591.28120.09930.439-0.16140.0460.25570.27270.7731-14.052-6.98783.5241
96.1044.3889-1.44914.7387-2.39827.69961.0018-0.66371.92930.0012-0.81583.1707-1.5650.1410.03730.92390.0383-0.18470.7526-0.02311.4071-37.9977-4.43163.2489
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 146 through 158 )A146 - 158
2X-RAY DIFFRACTION2chain 'A' and (resid 159 through 169 )A159 - 169
3X-RAY DIFFRACTION3chain 'A' and (resid 170 through 201 )A170 - 201
4X-RAY DIFFRACTION4chain 'A' and (resid 202 through 243 )A202 - 243
5X-RAY DIFFRACTION5chain 'A' and (resid 244 through 259 )A244 - 259
6X-RAY DIFFRACTION6chain 'A' and (resid 260 through 270 )A260 - 270
7X-RAY DIFFRACTION7chain 'A' and (resid 271 through 285 )A271 - 285
8X-RAY DIFFRACTION8chain 'A' and (resid 286 through 329 )A286 - 329
9X-RAY DIFFRACTION9chain 'A' and (resid 330 through 346 )A330 - 346

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