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- PDB-4oya: Human solAC Complexed with (4-Aminofurazan-3-yl)-[3-(1H-benzoimid... -

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Basic information

Entry
Database: PDB / ID: 4oya
TitleHuman solAC Complexed with (4-Aminofurazan-3-yl)-[3-(1H-benzoimidazol-2-ylmethoxy)phenyl]methanone
ComponentsAdenylate cyclase type 10
KeywordsLYASE
Function / homology
Function and homology information


negative regulation of cardiac muscle cell contraction / mitochondrial ATP transmembrane transport / bicarbonate binding / epithelial cilium movement involved in extracellular fluid movement / neuron projection retraction / astrocyte end-foot / central region of growth cone / positive regulation of glycogen catabolic process / glucose catabolic process / regulation of mitophagy ...negative regulation of cardiac muscle cell contraction / mitochondrial ATP transmembrane transport / bicarbonate binding / epithelial cilium movement involved in extracellular fluid movement / neuron projection retraction / astrocyte end-foot / central region of growth cone / positive regulation of glycogen catabolic process / 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 / neuron projection extension / positive regulation of protein targeting to mitochondrion / positive regulation of vascular associated smooth muscle cell apoptotic process / positive regulation of cardiac muscle hypertrophy / positive regulation of mitochondrial depolarization / positive regulation of reactive oxygen species biosynthetic process / negative regulation of mitochondrial membrane potential / positive regulation of ATP biosynthetic process / spermatid development / positive regulation of axon extension / positive regulation of cardiac muscle cell apoptotic process / Hedgehog 'off' state / negative regulation of reactive oxygen species biosynthetic process / neuron projection maintenance / apical part of cell / manganese ion binding / ATPase binding / cytoskeleton / intracellular signal transduction / cilium / neuronal cell body / dendrite / perinuclear region of cytoplasm / magnesium ion binding / mitochondrion / extracellular region / ATP binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Adenylate cyclase, type 10 / Nucleotide cyclase, GGDEF domain / Adenylate and Guanylate cyclase catalytic domain / Adenylyl cyclase class-3/4/guanylyl cyclase / Guanylate cyclase domain profile. / Nucleotide cyclase / Alpha-Beta Plaits / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-1VE / Adenylate cyclase type 10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.03 Å
AuthorsVinkovic, M.
CitationJournal: Chemmedchem / Year: 2014
Title: Crystal structure of human soluble adenylate cyclase reveals a distinct, highly flexible allosteric bicarbonate binding pocket.
Authors: Saalau-Bethell, S.M. / Berdini, V. / Cleasby, A. / Congreve, M. / Coyle, J.E. / Lock, V. / Murray, C.W. / O'Brien, M.A. / Rich, S.J. / Sambrook, T. / Vinkovic, M. / Yon, J.R. / Jhoti, H.
History
DepositionFeb 11, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 2, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Database references
Revision 1.2Feb 25, 2015Group: Derived calculations
Revision 1.3Nov 8, 2017Group: Derived calculations / Other ...Derived calculations / Other / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_database_status ...entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / software / struct_site / symmetry
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _software.classification / _struct_site.details / _symmetry.Int_Tables_number
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Adenylate cyclase type 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8943
Polymers53,4671
Non-polymers4272
Water9,890549
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area430 Å2
ΔGint-0 kcal/mol
Surface area21690 Å2
2
A: Adenylate cyclase type 10
hetero molecules

A: Adenylate cyclase type 10
hetero molecules

A: Adenylate cyclase type 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,6839
Polymers160,4003
Non-polymers1,2826
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area9100 Å2
ΔGint-49 kcal/mol
Surface area57240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.669, 99.669, 98.175
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#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: 53466.832 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADCY10, SAC / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q96PN6, adenylate cyclase
#2: Chemical ChemComp-1VE / (4-azanyl-1,2,5-oxadiazol-3-yl)-[3-(1H-benzimidazol-2-ylmethoxy)phenyl]methanone


Mass: 335.317 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H13N5O3
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 549 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 53.28 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 1ul of protein solution was mixed with 1ul of reservoir solution (0.1M sodium acetate, pH 4.8, 0.2M trisodium citrate, 16-18% PEG4K and 10% glycerol) and left to equilibrate at 4C

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.0332 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 21, 2006
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.03→28.77 Å / Num. obs: 35499 / % possible obs: 99.5 % / Redundancy: 2.6 % / Biso Wilson estimate: 25.15 Å2 / Net I/σ(I): 13.4

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
BUSTER-TNTBUSTER 2.11.5refinement
PDB_EXTRACT3.14data extraction
BUSTER2.11.5refinement
RefinementResolution: 2.03→28.77 Å / Cor.coef. Fo:Fc: 0.9534 / Cor.coef. Fo:Fc free: 0.9236 / SU R Cruickshank DPI: 0.161 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.174 / SU Rfree Blow DPI: 0.154 / SU Rfree Cruickshank DPI: 0.149
RfactorNum. reflection% reflectionSelection details
Rfree0.21 1780 5.01 %RANDOM
Rwork0.1611 ---
obs0.1636 35499 99.21 %-
Displacement parametersBiso mean: 32.751 Å2
Baniso -1Baniso -2Baniso -3
1--1.0121 Å20 Å20 Å2
2---1.0121 Å20 Å2
3---2.0242 Å2
Refine analyzeLuzzati coordinate error obs: 0.207 Å
Refinement stepCycle: 1 / Resolution: 2.03→28.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3767 0 31 549 4347
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0123935HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.065337HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1376SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes98HARMONIC2
X-RAY DIFFRACTIONt_gen_planes582HARMONIC16
X-RAY DIFFRACTIONt_it3929HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion6.43
X-RAY DIFFRACTIONt_other_torsion18.47
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion500SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5054SEMIHARMONIC4
LS refinement shellResolution: 2.03→2.09 Å / Total num. of bins used: 18
RfactorNum. reflection% reflection
Rfree0.2254 141 5 %
Rwork0.1932 2681 -
all0.1949 2822 -
obs--99.21 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4006-0.08290.22820.4591-0.16640.6304-0.0277-0.02590.0030.02210.05150.1254-0.047-0.1524-0.0238-0.06260.01780.0074-0.02870.0228-0.03121.717725.4965-2.1454
20.1986-0.0367-0.1017-0.1086-0.115700.0003-0.001-0.0072-0.0031-0.00210.0032-0.0059-0.00460.0018-0.0174-0.00060.02240.01270.03380.006217.15125.5913-3.1873
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|0 - A|468 }
2X-RAY DIFFRACTION2{ A|501 - A|501 }

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