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- PDB-4oyx: Human solAC Complexed with AMPCPP -

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Basic information

Entry
Database: PDB / ID: 4oyx
TitleHuman solAC Complexed with AMPCPP
ComponentsAdenylate cyclase type 10
KeywordsLYASE / protein-substrate analogue complex
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 / positive regulation of ATP biosynthetic process / negative regulation of mitochondrial membrane potential / 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 / cytosol / cytoplasm
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
DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / Adenylate cyclase type 10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.89 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 13, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 2, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Database references
Revision 1.2Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_oper_list / refine_hist / struct_conn / symmetry
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _symmetry.Int_Tables_number
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)54,0484
Polymers53,4671
Non-polymers5813
Water7,782432
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-26 kcal/mol
Surface area21300 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)162,14312
Polymers160,4003
Non-polymers1,7429
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 area11840 Å2
ΔGint-125 kcal/mol
Surface area55760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.651, 99.651, 96.522
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-974-

HOH

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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-APC / DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-CPP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 432 / 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

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Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.46 %
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: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Apr 8, 2005
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.89→49.83 Å / Num. obs: 28765 / % possible obs: 65.7 % / Redundancy: 3 % / Biso Wilson estimate: 30.55 Å2 / Net I/σ(I): 14.9

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Processing

SoftwareName: BUSTER / Version: 2.11.5 / Classification: refinement
RefinementResolution: 1.89→39.39 Å / Cor.coef. Fo:Fc: 0.9587 / Cor.coef. Fo:Fc free: 0.9292 / SU R Cruickshank DPI: 0.216 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.232 / SU Rfree Blow DPI: 0.194 / SU Rfree Cruickshank DPI: 0.19
RfactorNum. reflection% reflectionSelection details
Rfree0.2299 1444 5.02 %RANDOM
Rwork0.1682 ---
obs0.1714 28765 66.03 %-
Displacement parametersBiso mean: 52.812 Å2
Baniso -1Baniso -2Baniso -3
1--0.1144 Å20 Å20 Å2
2---0.1144 Å20 Å2
3---0.2288 Å2
Refine analyzeLuzzati coordinate error obs: 0.247 Å
Refinement stepCycle: 1 / Resolution: 1.89→39.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3734 0 33 432 4199
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0123878HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.225253HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1350SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes95HARMONIC2
X-RAY DIFFRACTIONt_gen_planes571HARMONIC16
X-RAY DIFFRACTIONt_it3872HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion7.23
X-RAY DIFFRACTIONt_other_torsion19.94
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion498SEMIHARMONIC5
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_contact5000SEMIHARMONIC4
LS refinement shellResolution: 1.89→1.96 Å / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.2245 14 4.14 %
Rwork0.2953 324 -
all0.2924 338 -
obs--66.03 %
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)
11.0285-0.0070.39270.7519-0.08930.9481-0.0486-0.05720.0863-0.01110.1090.2262-0.0433-0.2276-0.0604-0.1280.0152-0.0116-0.05860.08290.006721.800225.691-2.2197
20.10740.01130.20060.01120.1440-0.00620.0010.00290.0064-0.00040.00230.0021-0.00870.0066-0.02380.01530.0075-0.0072-0.02050.040817.343133.9604-5.9625
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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