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- PDB-9f1y: Crystal structure of Oscillatoria acuminata adenylyate cyclase at 100K -

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Basic information

Entry
Database: PDB / ID: 9f1y
TitleCrystal structure of Oscillatoria acuminata adenylyate cyclase at 100K
ComponentsFamily 3 adenylate cyclase
KeywordsLYASE / FAD / / adenylate cyclase
Function / homology
Function and homology information


cyclic nucleotide biosynthetic process / blue light photoreceptor activity / adenylate cyclase activity / FAD binding / ATP binding / metal ion binding
Similarity search - Function
: / BLUF domain profile. / BLUF domain / Sensors of blue-light using FAD / Sensors of blue-light using FAD / Acylphosphatase-like domain superfamily / Adenylyl- / guanylyl cyclase, catalytic domain / Adenylate and Guanylate cyclase catalytic domain / Adenylyl cyclase class-3/4/guanylyl cyclase / Guanylate cyclase domain profile. / Nucleotide cyclase
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Family 3 adenylate cyclase
Similarity search - Component
Biological speciesOscillatoria acuminata (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsKapetanaki, S. / Coquelle, N. / Weik, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To be published
Title: SSX room temperature structure of Oscillatoria acuminata adenylyate cyclase.
Authors: Kapetanaki, S. / Coquelle, N. / Weik, M.
History
DepositionApr 20, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Family 3 adenylate cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0394
Polymers44,1731
Non-polymers8663
Water3,585199
1
A: Family 3 adenylate cyclase
hetero molecules

A: Family 3 adenylate cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,0788
Polymers88,3472
Non-polymers1,7316
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area10260 Å2
ΔGint-121 kcal/mol
Surface area29310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.284, 53.455, 71.840
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Family 3 adenylate cyclase


Mass: 44173.285 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oscillatoria acuminata (bacteria) / Gene: Oscil6304_3613 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: K9TLZ5
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.51 Å3/Da / Density % sol: 51.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.06 M divalents, 0.1 M Tris-Bicine, 30% v/v PEG550 MME-PEG20000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Sep 12, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.95→47.27 Å / Num. obs: 29158 / % possible obs: 99.9 % / Redundancy: 6.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.034 / Rrim(I) all: 0.086 / Χ2: 0.96 / Net I/σ(I): 14.5 / Num. measured all: 186652
Reflection shellResolution: 1.95→2 Å / % possible obs: 99.8 % / Redundancy: 6.5 % / Rmerge(I) obs: 1.225 / Num. measured all: 13233 / Num. unique obs: 2022 / CC1/2: 0.702 / Rpim(I) all: 0.514 / Rrim(I) all: 1.331 / Χ2: 0.96 / Net I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→47.27 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.1 / Phase error: 25.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2273 2808 5.18 %
Rwork0.198 --
obs0.1995 29158 98.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→47.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2745 0 33 199 2977
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082849
X-RAY DIFFRACTIONf_angle_d0.9213860
X-RAY DIFFRACTIONf_dihedral_angle_d11.181392
X-RAY DIFFRACTIONf_chiral_restr0.06449
X-RAY DIFFRACTIONf_plane_restr0.01490
LS refinement shellResolution: 1.95→1.98 Å
RfactorNum. reflection% reflection
Rfree0.3949 133 -
Rwork0.3549 2577 -
obs--99 %

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