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- PDB-9f1x: SSX room temperature structure of Oscillatoria acuminata adenylya... -

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Basic information

Entry
Database: PDB / ID: 9f1x
TitleSSX room temperature structure of Oscillatoria acuminata adenylyate cyclase.
ComponentsFamily 3 adenylate cyclase
KeywordsLYASE / FAD / SSX / TREXX / room temperature / 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 MONONUCLEOTIDE / Family 3 adenylate cyclase
Similarity search - Component
Biological speciesOscillatoria acuminata (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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

Downloads & links

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Assembly

Deposited unit
A: Family 3 adenylate cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7104
Polymers44,1731
Non-polymers5373
Water1,65792
1
A: Family 3 adenylate cyclase
hetero molecules

A: Family 3 adenylate cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,4208
Polymers88,3472
Non-polymers1,0736
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area10070 Å2
ΔGint-126 kcal/mol
Surface area29180 Å2
Unit cell
Length a, b, c (Å)101.510, 53.930, 72.050
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-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#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.: 92 / 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: batch mode / 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: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.978 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Oct 29, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.8→59 Å / Num. obs: 36950 / % possible obs: 100 % / Redundancy: 595 % / CC1/2: 0.9989 / R split: 0.074 / Net I/σ(I): 7.8
Reflection shellResolution: 1.8→1.86 Å / Num. unique obs: 3615 / CC1/2: 0.5667 / R split: 1.907

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
CrystFELdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→58.75 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / Phase error: 23.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2122 1820 4.94 %
Rwork0.1843 --
obs0.1856 36864 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→58.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2724 0 33 92 2849
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082929
X-RAY DIFFRACTIONf_angle_d0.973992
X-RAY DIFFRACTIONf_dihedral_angle_d10.328420
X-RAY DIFFRACTIONf_chiral_restr0.062466
X-RAY DIFFRACTIONf_plane_restr0.01508
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.850.38781200.38432449X-RAY DIFFRACTION91
1.85-1.910.36051470.33212628X-RAY DIFFRACTION100
1.91-1.970.32511500.29382672X-RAY DIFFRACTION100
1.97-2.040.28451320.27482672X-RAY DIFFRACTION100
2.04-2.120.28381520.2342693X-RAY DIFFRACTION100
2.12-2.220.24571210.20622698X-RAY DIFFRACTION100
2.22-2.330.24441450.19922690X-RAY DIFFRACTION100
2.33-2.480.24261140.20412719X-RAY DIFFRACTION100
2.48-2.670.2121570.20172694X-RAY DIFFRACTION100
2.67-2.940.22221430.18842710X-RAY DIFFRACTION100
2.94-3.370.23031570.18442744X-RAY DIFFRACTION100
3.37-4.240.16611280.15172785X-RAY DIFFRACTION100
4.24-58.750.17561540.15212890X-RAY DIFFRACTION100

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