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- PDB-5o5l: X-ray structure of a bacterial adenylyl cyclase soluble domain, s... -

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Basic information

Entry
Database: PDB / ID: 5o5l
TitleX-ray structure of a bacterial adenylyl cyclase soluble domain, solved at cryogenic temperature
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: 2.7 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
C: Adenylate cyclase
D: Adenylate cyclase
E: Adenylate cyclase
F: Adenylate cyclase
G: Adenylate cyclase
H: Adenylate cyclase
I: Adenylate cyclase
J: Adenylate cyclase
K: Adenylate cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)319,48050
Polymers310,47511
Non-polymers9,00539
Water3,909217
1
A: Adenylate cyclase
B: Adenylate cyclase
hetero molecules


  • defined by author&software
  • Evidence: assay for oligomerization, EPR Spectroscopy confirms dimerization of the soluble domain in the presence of a substrate analogue, equilibrium centrifugation, AUC confirms ligand-dependent ...Evidence: assay for oligomerization, EPR Spectroscopy confirms dimerization of the soluble domain in the presence of a substrate analogue, equilibrium centrifugation, AUC confirms ligand-dependent dimerization of the soluble domain
  • 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
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8860 Å2
ΔGint-100 kcal/mol
Surface area19510 Å2
MethodPISA
2
C: Adenylate cyclase
D: Adenylate cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,17510
Polymers56,4502
Non-polymers1,7258
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8790 Å2
ΔGint-96 kcal/mol
Surface area19700 Å2
MethodPISA
3
E: Adenylate cyclase
F: Adenylate cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,0799
Polymers56,4502
Non-polymers1,6287
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8640 Å2
ΔGint-79 kcal/mol
Surface area19630 Å2
MethodPISA
4
G: Adenylate cyclase
H: 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
Buried area8500 Å2
ΔGint-68 kcal/mol
Surface area19660 Å2
MethodPISA
5
I: Adenylate cyclase
J: 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
Buried area8360 Å2
ΔGint-67 kcal/mol
Surface area19720 Å2
MethodPISA
6
K: Adenylate cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9914
Polymers28,2251
Non-polymers7663
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint-17 kcal/mol
Surface area12970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.480, 84.120, 310.750
Angle α, β, γ (deg.)90.00, 103.87, 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 / Fragment: Soluble domain, UNP residues 203-429
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.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 217 / 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: 2.95 Å3/Da / Density % sol: 58.34 %
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: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.89 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.89 Å / Relative weight: 1
ReflectionResolution: 2.7→49.38 Å / Num. obs: 98383 / % possible obs: 98.51 % / Redundancy: 44.3 % / Biso Wilson estimate: 93.95 Å2 / Net I/σ(I): 22.3

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementResolution: 2.7→49.38 Å / Cor.coef. Fo:Fc: 0.894 / Cor.coef. Fo:Fc free: 0.878 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.726 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.668 / SU Rfree Blow DPI: 0.34 / SU Rfree Cruickshank DPI: 0.35
RfactorNum. reflection% reflectionSelection details
Rfree0.289 4920 5 %RANDOM
Rwork0.265 ---
obs0.267 98383 98.5 %-
Displacement parametersBiso mean: 135.55 Å2
Baniso -1Baniso -2Baniso -3
1-5.8876 Å20 Å2-6.8956 Å2
2---4.611 Å20 Å2
3----1.2766 Å2
Refine analyzeLuzzati coordinate error obs: 0.5 Å
Refinement stepCycle: 1 / Resolution: 2.7→49.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19050 0 514 217 19781
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00819910HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0526981HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d7074SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes450HARMONIC2
X-RAY DIFFRACTIONt_gen_planes3168HARMONIC5
X-RAY DIFFRACTIONt_it19910HARMONIC20
X-RAY DIFFRACTIONt_nbd19SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.36
X-RAY DIFFRACTIONt_other_torsion22.75
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion2474SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact21963SEMIHARMONIC4
LS refinement shellResolution: 2.7→2.77 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 347 5.01 %
Rwork0.245 6575 -
all0.247 6922 -
obs--94.83 %
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)
11.38260.0266-0.23852.92750.67193.91870.0490.3208-0.0092-0.3252-0.1712-0.3515-0.3731-0.17760.1223-0.090.026-0.0113-0.3665-0.0608-0.103322.2087-10.8905-1.4314
21.0674-0.2612-0.22462.95070.10082.7834-0.0791-0.1239-0.29970.3603-0.1976-0.20780.326-0.23670.27670.0036-0.067-0.0591-0.3747-0.0295-0.008220.154-23.021116.3179
32.28070.07820.09364.6396-0.20772.23770.4986-0.21660.2515-0.1347-0.42630.67730.0264-0.4378-0.07230.0229-0.0918-0.011-0.3918-0.0647-0.134816.931718.325132.5362
43.55480.5432-0.12933.28540.65034.590.5834-1.0912-0.17120.5101-0.4447-0.46820.2560.5574-0.1387-0.0413-0.2596-0.1298-0.31880.1184-0.407931.04989.398946.3801
513.34635.95791.16866.06760.15294.0440.4966-0.8951-0.35250.6388-0.56450.71420.05580.00650.0679-0.3054-0.3090.1747-0.4392-0.0165-0.4719-8.3489-1.827565.8012
61.44833.00342.93184.81911.73492.6710.1371-0.99150.54040.7885-0.39450.42510.2905-0.52530.2574-0.1362-0.28960.26710.2159-0.095-0.49981.628310.252980.9852
72.5206-0.4696-0.66954.11020.7062.39640.12670.0729-0.6355-0.3144-0.0441-0.434-0.15950.3316-0.0826-0.3743-0.30580.1654-0.5029-0.02940.147120.8081-30.673188.3823
88.62246.2586-1.97636.5842-2.74495.26120.0548-0.5195-0.2311-0.06450.0996-0.2406-0.27920.1068-0.1544-0.5878-0.368-0.1061-0.15830.2222-0.077712.697-26.1136108.3397
912.46384.0675-4.99464.4991-2.05297.0111-0.3096-0.61890.1969-0.36620.695-0.2148-0.0593-0.8419-0.3854-0.6377-0.29830.0562-0.0825-0.0598-0.277649.8231-3.0404109.8802
103.7235-2.19950.05633.0155-1.95544.54130.0071-0.2111-0.43110.4361-0.1972-0.52520.2342-0.56240.1901-0.6035-0.3020.0820.13110.1678-0.059152.1109-14.9856128.2773
111.071-0.9171.61920.3531-2.02872.88450.0252-0.30110.43790.2546-0.09510.4381-0.10520.59140.0698-0.5331-0.22240.23830.6079-0.2635-0.246625.42518.6115142.7965
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }
5X-RAY DIFFRACTION5{ E|* }
6X-RAY DIFFRACTION6{ F|* }
7X-RAY DIFFRACTION7{ G|* }
8X-RAY DIFFRACTION8{ H|* }
9X-RAY DIFFRACTION9{ I|* }
10X-RAY DIFFRACTION10{ J|* }
11X-RAY DIFFRACTION11{ K|* }

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