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- PDB-4yus: Crystal structure of photoactivated adenylyl cyclase of a cyanoba... -

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Basic information

Entry
Database: PDB / ID: 4yus
TitleCrystal structure of photoactivated adenylyl cyclase of a cyanobacteriaOscillatoria acuminata in hexagonal form
ComponentsFamily 3 adenylate cyclase
KeywordsLYASE / Photoactivation / Adenylate cyclase
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 speciesOscillatoria acuminata PCC 6304 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsPark, S.-Y. / Ohki, M. / Sugiyama, K. / Kawai, F. / Iseki, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Structural insight into photoactivation of an adenylate cyclase from a photosynthetic cyanobacterium
Authors: Ohki, M. / Sugiyama, K. / Kawai, F. / Tanaka, H. / Nihei, Y. / Unzai, S. / Takebe, M. / Matsunaga, S. / Adachi, S. / Shibayama, N. / Zhou, Z. / Koyama, R. / Ikegaya, Y. / Takahashi, T. / ...Authors: Ohki, M. / Sugiyama, K. / Kawai, F. / Tanaka, H. / Nihei, Y. / Unzai, S. / Takebe, M. / Matsunaga, S. / Adachi, S. / Shibayama, N. / Zhou, Z. / Koyama, R. / Ikegaya, Y. / Takahashi, T. / Tame, J.R.H. / Iseki, M. / Park, S.-Y.
History
DepositionMar 19, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 1, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2016Group: Database references
Revision 1.2Jun 29, 2016Group: Database references
Revision 1.3Feb 5, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Mar 20, 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: Family 3 adenylate cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5102
Polymers43,0541
Non-polymers4561
Water2,702150
1
A: Family 3 adenylate cyclase
hetero molecules

A: Family 3 adenylate cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,0214
Polymers86,1082
Non-polymers9132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area8840 Å2
ΔGint-78 kcal/mol
Surface area29610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.838, 76.838, 204.778
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-645-

HOH

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Components

#1: Protein Family 3 adenylate cyclase / Photoactivated adenylate cyclase


Mass: 43054.121 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oscillatoria acuminata PCC 6304 (bacteria)
Gene: Oscil6304_3613 / Production host: Escherichia coli (E. coli) / References: UniProt: K9TLZ5, adenylate cyclase
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.03 Å3/Da / Density % sol: 39.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M sodium citrate pH5.0, 10% PEG 20K, 5mM Mgnasium chloride, 5mM ApCpp

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 0.95 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 33448 / % possible obs: 97.7 % / Redundancy: 9.3 % / Net I/σ(I): 8.7

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1839)refinement
HKL-2000data scaling
PHASERphasing
RefinementResolution: 1.8→33.48 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.92 / Stereochemistry target values: ML
Details: the entry contains Friedel pairs in F_Plus/Minus columns
RfactorNum. reflection% reflection
Rfree0.2643 1620 4.86 %
Rwork0.2123 --
obs0.2147 31816 98.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→33.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2758 0 31 150 2939
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082832
X-RAY DIFFRACTIONf_angle_d1.1783829
X-RAY DIFFRACTIONf_dihedral_angle_d16.7281061
X-RAY DIFFRACTIONf_chiral_restr0.043443
X-RAY DIFFRACTIONf_plane_restr0.005485
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7989-1.82840.40221360.35212456X-RAY DIFFRACTION87
1.8284-1.85990.34121460.31162611X-RAY DIFFRACTION93
1.8599-1.89370.30011530.30142731X-RAY DIFFRACTION97
1.8937-1.93010.24971520.28422767X-RAY DIFFRACTION97
1.9301-1.96950.34051500.27072836X-RAY DIFFRACTION99
1.9695-2.01230.34641070.27012834X-RAY DIFFRACTION99
2.0123-2.05920.27261600.25592790X-RAY DIFFRACTION100
2.0592-2.11060.28661650.23842817X-RAY DIFFRACTION99
2.1106-2.16770.24081190.21712861X-RAY DIFFRACTION99
2.1677-2.23150.32471560.2222827X-RAY DIFFRACTION100
2.2315-2.30350.26271390.2212830X-RAY DIFFRACTION100
2.3035-2.38580.26821340.2142848X-RAY DIFFRACTION100
2.3858-2.48130.25561500.22662839X-RAY DIFFRACTION99
2.4813-2.59420.22931240.22942833X-RAY DIFFRACTION100
2.5942-2.73090.2641270.22142872X-RAY DIFFRACTION100
2.7309-2.90190.28941460.21872826X-RAY DIFFRACTION100
2.9019-3.12580.26051490.22452840X-RAY DIFFRACTION100
3.1258-3.44010.2071740.19362809X-RAY DIFFRACTION100
3.4401-3.93720.22351500.18152840X-RAY DIFFRACTION100
3.9372-4.95790.27421130.17112854X-RAY DIFFRACTION99
4.9579-33.4860.27361500.19492813X-RAY DIFFRACTION99

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