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- PDB-5x4u: PAC from Oscillatoriaacuminata after 60 seconds photoactivation -

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Basic information

Entry
Database: PDB / ID: 5x4u
TitlePAC from Oscillatoriaacuminata after 60 seconds photoactivation
ComponentsPhotoactivated adenylyl cyclase
KeywordsLYASE / cAMP / BLUF domain / optogenetics / photoactivation / allostery
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 speciesCyanobacteria (blue-green algae)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsOhki, M. / Park, S.-Y.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Molecular mechanism of photoactivation of a light-regulated adenylate cyclase.
Authors: Ohki, M. / Sato-Tomita, A. / Matsunaga, S. / Iseki, M. / Tame, J.R.H. / Shibayama, N. / Park, S.Y.
History
DepositionFeb 14, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 26, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Mar 27, 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: Photoactivated adenylyl cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4752
Polymers41,0191
Non-polymers4561
Water4,846269
1
A: Photoactivated adenylyl cyclase
hetero molecules

A: Photoactivated adenylyl cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,9504
Polymers82,0382
Non-polymers9132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area8780 Å2
ΔGint-78 kcal/mol
Surface area29400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.149, 77.149, 204.824
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Photoactivated adenylyl cyclase


Mass: 41018.828 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cyanobacteria (blue-green algae) / Production host: Cyanobacteria (blue-green algae) / References: UniProt: K9TLZ5*PLUS
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C17H21N4O9P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 269 / Source method: isolated from a natural source / Formula: H2O

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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: 2.24 Å3/Da / Density % sol: 45.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100mM Sodium Citrate pH5.0, 10% PEG 20000, 5mM ApCpp, 2mM MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 33703 / % possible obs: 97.9 % / Redundancy: 11.4 % / Net I/σ(I): 33.2

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPmodel building
RefinementResolution: 1.8→34.923 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.43 / Phase error: 22.18
RfactorNum. reflection% reflection
Rfree0.2449 1704 5.06 %
Rwork0.2026 --
obs0.2047 33674 98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→34.923 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2758 0 31 271 3060
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082832
X-RAY DIFFRACTIONf_angle_d0.963829
X-RAY DIFFRACTIONf_dihedral_angle_d21.2981719
X-RAY DIFFRACTIONf_chiral_restr0.06443
X-RAY DIFFRACTIONf_plane_restr0.005485
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8005-1.85350.31221210.3132312X-RAY DIFFRACTION87
1.8535-1.91330.35081490.2952487X-RAY DIFFRACTION94
1.9133-1.98160.30721210.25762632X-RAY DIFFRACTION98
1.9816-2.0610.29921480.23662637X-RAY DIFFRACTION100
2.061-2.15480.25381520.20732670X-RAY DIFFRACTION100
2.1548-2.26840.26111460.19562672X-RAY DIFFRACTION100
2.2684-2.41040.24111470.19332677X-RAY DIFFRACTION100
2.4104-2.59650.24631290.1972699X-RAY DIFFRACTION100
2.5965-2.85770.24051600.1922708X-RAY DIFFRACTION100
2.8577-3.27090.22461480.19882734X-RAY DIFFRACTION100
3.2709-4.120.23821390.17772795X-RAY DIFFRACTION100
4.12-34.92970.21021440.19132947X-RAY DIFFRACTION98

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