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- PDB-5o5k: X-ray structure of a bacterial adenylyl cyclase soluble domain -

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Basic information

Entry
Database: PDB / ID: 5o5k
TitleX-ray structure of a bacterial adenylyl cyclase soluble domain
ComponentsAdenylate cyclaseAdenylyl cyclase
KeywordsMEMBRANE PROTEIN / membrane-integral adenylyl cyclase / helical domain / catalytic domain / MANT-GTP
Function / homology
Function and homology information


cyclic nucleotide biosynthetic process / adenylate cyclase / adenylate cyclase activity / intracellular signal transduction / membrane
Similarity search - Function
Nucleotide cyclase, GGDEF domain / Adenylyl cyclase class-4/guanylyl cyclase, conserved site / Guanylate cyclase signature. / Adenylyl- / guanylyl cyclase, catalytic domain / Adenylyl cyclase class-3/4/guanylyl cyclase / Adenylate and Guanylate cyclase catalytic domain / Guanylate cyclase domain profile. / Nucleotide cyclase / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Chem-ONM / Adenylate cyclase
Similarity search - Component
Biological speciesMycobacterium intracellulare 1956 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.4 Å
AuthorsVercellino, I. / Korkhov, V.M.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation150665 Switzerland
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Role of the nucleotidyl cyclase helical domain in catalytically active dimer formation.
Authors: Vercellino, I. / Rezabkova, L. / Olieric, V. / Polyhach, Y. / Weinert, T. / Kammerer, R.A. / Jeschke, G. / Korkhov, V.M.
History
DepositionJun 2, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 1, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Nov 22, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 16, 2019Group: Data collection / Category: reflns_shell

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Adenylate cyclase
B: Adenylate cyclase
D: Adenylate cyclase
C: Adenylate cyclase
E: Adenylate cyclase
F: Adenylate cyclase
I: Adenylate cyclase
J: Adenylate cyclase
H: Adenylate cyclase
G: Adenylate cyclase
K: Adenylate cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)320,15257
Polymers310,47511
Non-polymers9,67746
Water0
1
A: Adenylate cyclase
B: Adenylate cyclase
hetero molecules


  • defined by author&software
  • Evidence: assay for oligomerization, EPR Spectroscopy confirms dimerization of soluble domain in the presence of substrate analogue, equilibrium centrifugation, AUC Confirms ligand-dependent dimerization of the protein
  • 58.3 kDa, 2 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)58,27111
Polymers56,4502
Non-polymers1,8219
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
D: Adenylate cyclase
C: Adenylate cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,27111
Polymers56,4502
Non-polymers1,8219
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
E: Adenylate cyclase
F: Adenylate cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,27111
Polymers56,4502
Non-polymers1,8219
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
H: Adenylate cyclase
G: Adenylate cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,0799
Polymers56,4502
Non-polymers1,6287
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
I: Adenylate cyclase
J: Adenylate cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,27111
Polymers56,4502
Non-polymers1,8219
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
K: Adenylate cyclase
hetero molecules

K: Adenylate cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9828
Polymers56,4502
Non-polymers1,5326
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_759-x+2,y,-z+41
MethodPISA
Unit cell
Length a, b, c (Å)145.420, 85.690, 318.010
Angle α, β, γ (deg.)90.00, 103.77, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Adenylate cyclase / Adenylyl cyclase


Mass: 28225.025 Da / Num. of mol.: 11
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium intracellulare 1956 (bacteria)
Gene: cya, I550_3099 / Production host: Escherichia coli (E. coli) / References: UniProt: X8CHM4, adenylate cyclase
#2: Chemical
ChemComp-ONM / 3'-O-(N-METHYLANTHRANILOYL)-GUANOSINE-5'-TRIPHOSPHATE


Mass: 656.328 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C18H23N6O15P3
#3: Chemical...
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: Mn
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4

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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: 3.1 Å3/Da / Density % sol: 60.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M NaCacodylate pH 6.5, 0.2 M LiSO4, 8-10% PEG 1000, 8-10% PEG 8000

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Oct 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→46.85 Å / Num. obs: 62261 / % possible obs: 98 % / Redundancy: 5.9 % / Net I/σ(I): 4.11

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementResolution: 3.4→47.303 Å / SU ML: 0.54 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2658 2001 3.85 %
Rwork0.245 --
obs0.2459 51912 98.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.4→47.303 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18370 0 549 0 18919
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01219258
X-RAY DIFFRACTIONf_angle_d1.56926104
X-RAY DIFFRACTIONf_dihedral_angle_d26.7227029
X-RAY DIFFRACTIONf_chiral_restr0.0832838
X-RAY DIFFRACTIONf_plane_restr0.0093333
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4001-3.48510.35661380.32193534X-RAY DIFFRACTION98
3.4851-3.57930.34571440.31553544X-RAY DIFFRACTION99
3.5793-3.68450.30561450.31753596X-RAY DIFFRACTION99
3.6845-3.80340.32391420.29393495X-RAY DIFFRACTION99
3.8034-3.93930.28631390.28343549X-RAY DIFFRACTION99
3.9393-4.09690.30631440.2823531X-RAY DIFFRACTION97
4.0969-4.28330.30921410.27543559X-RAY DIFFRACTION98
4.2833-4.50890.25181380.24363542X-RAY DIFFRACTION98
4.5089-4.79120.26261450.23413547X-RAY DIFFRACTION99
4.7912-5.16070.26571440.22163581X-RAY DIFFRACTION99
5.1607-5.67930.27811470.23893604X-RAY DIFFRACTION98
5.6793-6.49930.28571380.25953591X-RAY DIFFRACTION99
6.4993-8.18150.22671460.23133551X-RAY DIFFRACTION97
8.1815-47.3080.20941500.19033687X-RAY DIFFRACTION98
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)
10.1061-0.07070.10590.1123-0.06820.29170.0087-0.1560.1204-0.04490.03-0.19230.0887-0.11130.01540.5401-0.0297-0.01980.3235-0.08490.5719-20.9217-56.3224773.7574
20.2890.13360.20740.1904-0.09090.47810.2169-0.00040.1818-0.2926-0.1131-0.0069-0.1854-0.23090.05430.54270.05750.15270.270.01270.6904-23.1102-44.595755.795
30.2468-0.024-0.15670.1517-0.0330.16550.09940.0613-0.1010.0572-0.0430.1980.0032-0.2507-0.00050.42840.0813-0.0520.31690.01030.562-25.4952-87.1302738.6582
40.13750.104-0.01480.1455-0.0370.21230.19230.36720.0355-0.3259-0.1421-0.0373-0.08270.188-0.06590.69510.16650.06870.5927-0.00120.4608-11.2554-78.3402724.9725
50.09160.0605-0.05220.2078-0.06280.02140.43180.2731-0.1907-0.2454-0.30980.2453-0.0937-0.09860.02920.7240.4784-0.03261.0703-0.06470.663-51.3857-66.6576704.5093
60.22390.2288-0.19920.3845-0.16170.20490.5630.6493-0.1705-0.2278-0.39160.2133-0.26670.05210.16811.06530.6729-0.23711.3924-0.19670.7533-41.892-78.7809689.4001
70.1541-0.1313-0.14930.13360.13090.17480.33570.160.5306-0.0140.1541-0.0933-0.16030.21170.34671.10561.14280.62631.10990.52311.2221-22.2882-37.0834680.5422
80.0997-0.06940.09140.0325-0.08220.1332-0.09570.08490.32120.01590.19010.1825-0.0571-0.1401-0.19980.731.35480.5932.2220.93261.2633-29.9686-41.9627661.0142
90.1160.1367-0.15080.6601-0.5390.44550.30750.3753-0.43430.71910.9415-0.11240.2109-0.21081.0880.83271.2666-0.49111.9651-0.37431.01748.8744-66.1271659.7563
100.4033-0.1349-0.10090.3840.05080.0625-0.0462-0.02340.30210.18240.9827-0.35890.07-0.34140.26820.74160.4183-0.09282.184-0.34021.117211.4578-55.1932642.5005
110.12330.0351-0.08950.0877-0.03170.0420.3477-0.0922-0.3808-0.18120.00470.09130.48890.0968-0.01311.7718-0.0516-0.75452.27780.02221.386-15.5626-87.7856625.6579
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A'
2X-RAY DIFFRACTION2chain 'B'
3X-RAY DIFFRACTION3chain 'C'
4X-RAY DIFFRACTION4chain 'D'
5X-RAY DIFFRACTION5chain 'E'
6X-RAY DIFFRACTION6chain 'F'
7X-RAY DIFFRACTION7chain 'G'
8X-RAY DIFFRACTION8chain 'H'
9X-RAY DIFFRACTION9chain 'I'
10X-RAY DIFFRACTION10chain 'J'
11X-RAY DIFFRACTION11chain 'K'

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