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- PDB-4yut: Crystal structure of photoactivated adenylyl cyclase of a cyanoba... -

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Basic information

Entry
Database: PDB / ID: 4yut
TitleCrystal structure of photoactivated adenylyl cyclase of a cyanobacteriaOscillatoria acuminata in orthorhombic form
ComponentsFamily 3 adenylate cyclase
KeywordsLYASE / Photoactivation / Adenylate cyclase
Function / homology
Function and homology information


cyclic nucleotide biosynthetic process / blue light photoreceptor activity / adenylate cyclase activity / FAD binding / cell projection / intracellular signal transduction
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 / Family 3 adenylate cyclase
Similarity search - Component
Biological speciesOscillatoria acuminata PCC 6304 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.9 Å
AuthorsPark, S.-Y. / Ohki, M. / Sugiyama, K. / Kawai, F. / Iseki, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Structural insight into photoactivation of an adenylate cyclase from a photosynthetic cyanobacterium
Authors: Ohki, M. / Sugiyama, K. / Kawai, F. / Tanaka, H. / Nihei, Y. / Unzai, S. / Takebe, M. / Matsunaga, S. / Adachi, S. / Shibayama, N. / Zhou, Z. / Koyama, R. / Ikegaya, Y. / Takahashi, T. / ...Authors: Ohki, M. / Sugiyama, K. / Kawai, F. / Tanaka, H. / Nihei, Y. / Unzai, S. / Takebe, M. / Matsunaga, S. / Adachi, S. / Shibayama, N. / Zhou, Z. / Koyama, R. / Ikegaya, Y. / Takahashi, T. / Tame, J.R.H. / Iseki, M. / Park, S.-Y.
History
DepositionMar 19, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 1, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2016Group: Database references
Revision 1.2Jun 29, 2016Group: Database references
Revision 1.3Feb 5, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Family 3 adenylate cyclase
B: Family 3 adenylate cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,0214
Polymers86,1082
Non-polymers9132
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9640 Å2
ΔGint-82 kcal/mol
Surface area30320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.351, 100.699, 120.673
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Family 3 adenylate cyclase / Photoactivated adenylate cyclase


Mass: 43054.121 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oscillatoria acuminata PCC 6304 (bacteria)
Gene: Oscil6304_3613 / Production host: Escherichia coli (E. coli) / References: UniProt: K9TLZ5, adenylate cyclase
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.01 Å3/Da / Density % sol: 59.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M sodium citrate pH5.0, 10% PEG 20K, 10mM sodium malonate pH7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.9 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 22797 / % possible obs: 96.1 % / Redundancy: 4.6 % / Biso Wilson estimate: 58.7 Å2 / Net I/σ(I): 14.9

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 2.9→43.79 Å / Cor.coef. Fo:Fc: 0.8444 / Cor.coef. Fo:Fc free: 0.8126 / SU R Cruickshank DPI: 3.039 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 2.455 / SU Rfree Blow DPI: 0.44 / SU Rfree Cruickshank DPI: 0.45
RfactorNum. reflection% reflectionSelection details
Rfree0.3098 1205 5.29 %RANDOM
Rwork0.2712 ---
obs0.2733 22775 96.21 %-
Displacement parametersBiso mean: 99.81 Å2
Baniso -1Baniso -2Baniso -3
1--27.5516 Å20 Å20 Å2
2--13.3481 Å20 Å2
3---14.2034 Å2
Refine analyzeLuzzati coordinate error obs: 0.569 Å
Refinement stepCycle: 1 / Resolution: 2.9→43.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5536 0 62 0 5598
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0095686HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.127688HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2056SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes154HARMONIC2
X-RAY DIFFRACTIONt_gen_planes854HARMONIC5
X-RAY DIFFRACTIONt_it5686HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.1
X-RAY DIFFRACTIONt_other_torsion23.82
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion774SEMIHARMONIC5
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_contact6693SEMIHARMONIC4
LS refinement shellResolution: 2.9→3.04 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.256 132 4.59 %
Rwork0.2619 2745 -
all0.2616 2877 -
obs--96.21 %

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