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- PDB-5d0r: Crystal structure of human soluble Adenylyl Cyclase with the inhi... -

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Basic information

Entry
Database: PDB / ID: 5d0r
TitleCrystal structure of human soluble Adenylyl Cyclase with the inhibitor bithionol
ComponentsAdenylate cyclase type 10
KeywordsLYASE
Function / homology
Function and homology information


negative regulation of cardiac muscle cell contraction / astrocyte end-foot / mitochondrial ATP transmembrane transport / bicarbonate binding / epithelial cilium movement involved in extracellular fluid movement / neuron projection retraction / positive regulation of glycogen catabolic process / : / central region of growth cone / glucose catabolic process ...negative regulation of cardiac muscle cell contraction / astrocyte end-foot / mitochondrial ATP transmembrane transport / bicarbonate binding / epithelial cilium movement involved in extracellular fluid movement / neuron projection retraction / positive regulation of glycogen catabolic process / : / central region of growth cone / glucose catabolic process / regulation of mitophagy / regulation of membrane repolarization / adenylate cyclase / basal part of cell / positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / cAMP biosynthetic process / positive regulation of ossification / adenylate cyclase activity / positive regulation of protein targeting to mitochondrion / positive regulation of reactive oxygen species biosynthetic process / neuron projection extension / positive regulation of vascular associated smooth muscle cell apoptotic process / positive regulation of mitochondrial depolarization / positive regulation of ATP biosynthetic process / positive regulation of cardiac muscle hypertrophy / positive regulation of cardiac muscle cell apoptotic process / negative regulation of mitochondrial membrane potential / spermatid development / positive regulation of axon extension / Hedgehog 'off' state / negative regulation of reactive oxygen species biosynthetic process / neuron projection maintenance / positive regulation of peptidyl-threonine phosphorylation / cilium / manganese ion binding / ATPase binding / cytoskeleton / intracellular signal transduction / apical plasma membrane / neuronal cell body / dendrite / perinuclear region of cytoplasm / magnesium ion binding / mitochondrion / extracellular region / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Adenylate cyclase, type 10 / Nucleotide cyclase, GGDEF domain / Adenylyl cyclase class-3/4/guanylyl cyclase / Adenylate and Guanylate cyclase catalytic domain / Guanylate cyclase domain profile. / Nucleotide cyclase / Alpha-Beta Plaits / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / 2,2'-sulfanediylbis(4,6-dichlorophenol) / Adenylate cyclase type 10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.24 Å
AuthorsKleinboelting, S. / Steegborn, C.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationSTE1701/11 Germany
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Bithionol Potently Inhibits Human Soluble Adenylyl Cyclase through Binding to the Allosteric Activator Site.
Authors: Kleinboelting, S. / Ramos-Espiritu, L. / Buck, H. / Colis, L. / van den Heuvel, J. / Glickman, J.F. / Levin, L.R. / Buck, J. / Steegborn, C.
History
DepositionAug 3, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 16, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2016Group: Database references
Revision 1.2May 11, 2016Group: Database references
Revision 2.0Mar 27, 2019Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Source and taxonomy
Category: atom_site / database_PDB_rev ...atom_site / database_PDB_rev / database_PDB_rev_record / entity_src_gen / pdbx_audit_support / pdbx_nonpoly_scheme / pdbx_solvent_atom_site_mapping
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.pdbx_auth_seq_id / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain / _pdbx_audit_support.funding_organization / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_solvent_atom_site_mapping.auth_seq_id
Revision 2.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Adenylate cyclase type 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,47614
Polymers54,2701
Non-polymers1,20613
Water3,855214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2780 Å2
ΔGint24 kcal/mol
Surface area20260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.403, 99.403, 99.978
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-812-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Adenylate cyclase type 10 / AH-related protein / Adenylate cyclase homolog / Germ cell soluble adenylyl cyclase / sAC / ...AH-related protein / Adenylate cyclase homolog / Germ cell soluble adenylyl cyclase / sAC / Testicular soluble adenylyl cyclase


Mass: 54269.664 Da / Num. of mol.: 1 / Fragment: catalytic domain, UNP residues 1-469
Source method: isolated from a genetically manipulated source
Details: Cys255 modified by beta-mercaptoethanol / Source: (gene. exp.) Homo sapiens (human) / Gene: ADCY10, SAC / Plasmid: PVL1392 / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q96PN6, adenylate cyclase

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Non-polymers , 6 types, 227 molecules

#2: Chemical ChemComp-B1T / 2,2'-sulfanediylbis(4,6-dichlorophenol)


Mass: 356.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H6Cl4O2S / Comment: antibiotic*YM
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / 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: 2.63 Å3/Da / Density % sol: 53.25 % / Description: rockets
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1 M SODIUM ACETATE PH 4.8, 0.2 M TRI-SODIUM-CITRATE, 15% (W/V) PEG 4000, 10% (V/V) GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 10, 2014 / Details: COLLIMATOR
RadiationMonochromator: SI111-DCM WITH SAGITTAL BENDER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.24→86.23 Å / Num. obs: 27051 / % possible obs: 100 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.0138 / Net I/σ(I): 11.9
Reflection shellResolution: 2.24→2.37 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.0894 / Mean I/σ(I) obs: 1.7 / % possible all: 99

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
XSCALEdata scaling
MOLREPphasing
REFMAC5.8.0124refinement
PDB_EXTRACT3.15data extraction
Cootmodel building
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CLK

4clk


Resolution: 2.24→86.23 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.912 / SU B: 14.431 / SU ML: 0.177 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.256 / ESU R Free: 0.218 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2437 1383 5.1 %RANDOM
Rwork0.1773 ---
obs0.1806 25668 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 107.27 Å2 / Biso mean: 35.966 Å2 / Biso min: 5.67 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å2-0.11 Å2-0 Å2
2---0.22 Å20 Å2
3---0.7 Å2
Refinement stepCycle: final / Resolution: 2.24→86.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3654 0 71 214 3939
Biso mean--47.97 39.34 -
Num. residues----461
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0193817
X-RAY DIFFRACTIONr_bond_other_d0.0020.023644
X-RAY DIFFRACTIONr_angle_refined_deg2.1771.9665149
X-RAY DIFFRACTIONr_angle_other_deg1.13438377
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6425463
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.29624.444171
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.21615646
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6171515
X-RAY DIFFRACTIONr_chiral_restr0.1310.2569
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214247
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02876
X-RAY DIFFRACTIONr_mcbond_it2.4022.8311847
X-RAY DIFFRACTIONr_mcbond_other2.3972.8271845
X-RAY DIFFRACTIONr_mcangle_it3.9464.2282305
LS refinement shellResolution: 2.238→2.296 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 99 -
Rwork0.281 1859 -
all-1958 -
obs--97.9 %
Refinement TLS params.Method: refined / Origin x: 21.2234 Å / Origin y: 25.365 Å / Origin z: 0.5942 Å
111213212223313233
T0.0204 Å20.0029 Å20.0061 Å2-0.0439 Å2-0.0017 Å2--0.0125 Å2
L0.4852 °20.0243 °20.0195 °2-0.3561 °2-0.0493 °2--0.6702 °2
S-0.013 Å °-0.0264 Å °-0.0055 Å °0.0107 Å °-0.0035 Å °0.0603 Å °-0.0147 Å °-0.0922 Å °0.0165 Å °

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