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- PDB-9f1w: SFX room temperature structure of Oscillatoria acuminata adenylya... -

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Basic information

Entry
Database: PDB / ID: 9f1w
TitleSFX room temperature structure of Oscillatoria acuminata adenylyate cyclase.
ComponentsFamily 3 adenylate cyclase
KeywordsLYASE / FAD / SFX / EuXFEL / room temperature / adenylate cyclase
Function / homology
Function and homology information


cyclic nucleotide biosynthetic process / blue light photoreceptor activity / adenylate cyclase activity / FAD binding / cell projection / ATP binding / metal ion binding
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 / 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 / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsKapetanaki, S. / Coquelle, N. / Weik, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To be published
Title: SFX 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)45,0394
Polymers44,1731
Non-polymers8663
Water2,036113
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 area9830 Å2
ΔGint-128 kcal/mol
Surface area30600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.900, 54.910, 72.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-608-

HOH

21A-613-

HOH

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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.: 113 / 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
Details: 0.06 M divalents, 0.1 M Tris-Bicine 8.5, 30% v/v PEG550 MME-PEG20000

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: European XFEL / Beamline: SPB/SFX / Wavelength: 1.33 Å
DetectorType: AGIPD / Detector: PIXEL / Date: Oct 26, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.33 Å / Relative weight: 1
ReflectionResolution: 1.75→27 Å / Num. obs: 42444 / % possible obs: 100 % / Redundancy: 453 % / CC1/2: 0.9905 / R split: 0.085 / Net I/σ(I): 7.4
Reflection shellResolution: 1.75→1.78 Å / Mean I/σ(I) obs: 1.1 / Num. unique obs: 2694 / CC1/2: 0.5868 / R split: 0.908
Serial crystallography measurementFocal spot size: 3 µm2 / Pulse duration: 50 fsec. / Pulse photon energy: 9.3 keV / XFEL pulse repetition rate: 564000 Hz
Serial crystallography sample deliveryDescription: GDVN / Method: injection

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158)refinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→26.53 Å / SU ML: 0.27 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 23.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2191 2046 4.82 %
Rwork0.1937 --
obs0.1949 42444 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→26.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2698 0 33 113 2844
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092868
X-RAY DIFFRACTIONf_angle_d0.8793912
X-RAY DIFFRACTIONf_dihedral_angle_d10.308409
X-RAY DIFFRACTIONf_chiral_restr0.065460
X-RAY DIFFRACTIONf_plane_restr0.009499
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.790.34061230.31422661X-RAY DIFFRACTION100
1.79-1.840.30621320.29342688X-RAY DIFFRACTION100
1.84-1.890.41451350.36562636X-RAY DIFFRACTION100
1.89-1.940.43411440.36432664X-RAY DIFFRACTION100
1.94-20.30341520.24512610X-RAY DIFFRACTION100
2-2.070.2641520.20342653X-RAY DIFFRACTION100
2.07-2.160.21941230.20352673X-RAY DIFFRACTION100
2.16-2.260.23831360.2112675X-RAY DIFFRACTION100
2.26-2.370.23391230.22242681X-RAY DIFFRACTION100
2.37-2.520.28311310.21042703X-RAY DIFFRACTION100
2.52-2.720.25211340.20272684X-RAY DIFFRACTION100
2.72-2.990.20071450.20282712X-RAY DIFFRACTION100
2.99-3.420.19961250.18112732X-RAY DIFFRACTION100
3.42-4.310.17911500.15792744X-RAY DIFFRACTION100
4.31-26.530.19561410.17622882X-RAY DIFFRACTION100

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