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- PDB-9f1z: Crystal structure of adenylyate cyclase variant Y6W -

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Basic information

Entry
Database: PDB / ID: 9f1z
TitleCrystal structure of adenylyate cyclase variant Y6W
ComponentsFamily 3 adenylate cyclase
KeywordsLYASE / FAD / mutant / Y6W / 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: 1.95 Å
AuthorsKapetanaki, S. / Coquelle, N. / Weik, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Iucrj / Year: 2024
Title: Crystal structure of a bacterial photoactivated adenylate cyclase determined by serial femtosecond and serial synchrotron crystallography.
Authors: Kapetanaki, S.M. / Coquelle, N. / von Stetten, D. / Byrdin, M. / Rios-Santacruz, R. / Bean, R. / Bielecki, J. / Boudjelida, M. / Fekete, Z. / Grime, G.W. / Han, H. / Hatton, C. / Kantamneni, ...Authors: Kapetanaki, S.M. / Coquelle, N. / von Stetten, D. / Byrdin, M. / Rios-Santacruz, R. / Bean, R. / Bielecki, J. / Boudjelida, M. / Fekete, Z. / Grime, G.W. / Han, H. / Hatton, C. / Kantamneni, S. / Kharitonov, K. / Kim, C. / Kloos, M. / Koua, F.H.M. / de Diego Martinez, I. / Melo, D. / Rane, L. / Round, A. / Round, E. / Sarma, A. / Schubert, R. / Schulz, J. / Sikorski, M. / Vakili, M. / Valerio, J. / Vitas, J. / de Wijn, R. / Wrona, A. / Zala, N. / Pearson, A. / Dorner, K. / Schiro, G. / Garman, E.F. / Lukacs, A. / Weik, M.
History
DepositionApr 20, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 26, 2025Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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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)40,0025
Polymers39,3731
Non-polymers6294
Water3,081171
1
A: Family 3 adenylate cyclase
hetero molecules

A: Family 3 adenylate cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,00310
Polymers78,7462
Non-polymers1,2578
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area10740 Å2
ΔGint-131 kcal/mol
Surface area28880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.455, 52.684, 71.525
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-671-

HOH

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Components

#1: Protein Family 3 adenylate cyclase


Mass: 39372.934 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 2.14 Å3/Da / Density % sol: 42.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.06 M divalents, 0.1 M Tris-Bicine pH 8.5, 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: Nov 11, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.95→46.66 Å / Num. obs: 27876 / % possible obs: 98.8 % / Redundancy: 3.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.032 / Rrim(I) all: 0.063 / Χ2: 0.97 / Net I/σ(I): 12.8 / Num. measured all: 106179
Reflection shellResolution: 1.95→2 Å / % possible obs: 97.8 % / Redundancy: 3.8 % / Rmerge(I) obs: 1.21 / Num. measured all: 7386 / Num. unique obs: 1924 / CC1/2: 0.48 / Rpim(I) all: 0.692 / Rrim(I) all: 1.405 / Χ2: 0.99 / Net I/σ(I) obs: 1.1

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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→46.66 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2335 1439 5.17 %
Rwork0.1958 --
obs0.1978 27835 98.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→46.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2755 0 39 171 2965
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082865
X-RAY DIFFRACTIONf_angle_d1.0483880
X-RAY DIFFRACTIONf_dihedral_angle_d13.541395
X-RAY DIFFRACTIONf_chiral_restr0.064447
X-RAY DIFFRACTIONf_plane_restr0.01493
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.020.4491460.39032580X-RAY DIFFRACTION98
2.02-2.10.36241350.29742637X-RAY DIFFRACTION99
2.1-2.20.28431410.2472655X-RAY DIFFRACTION100
2.2-2.310.27561450.22262633X-RAY DIFFRACTION99
2.31-2.460.31341350.21342641X-RAY DIFFRACTION99
2.46-2.650.27451360.21742674X-RAY DIFFRACTION99
2.65-2.910.23971410.20542661X-RAY DIFFRACTION100
2.91-3.330.26251560.19552642X-RAY DIFFRACTION98
3.33-4.20.18581510.16622638X-RAY DIFFRACTION97
4.2-46.660.19771530.17072635X-RAY DIFFRACTION92

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