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- PDB-1ab8: RAT TYPE II ADENYLYL CYCLASE C2 DOMAIN/FORSKOLIN COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1ab8
TitleRAT TYPE II ADENYLYL CYCLASE C2 DOMAIN/FORSKOLIN COMPLEX
ComponentsADENYLYL CYCLASE
KeywordsLYASE / ADENYLYL CYCLASE / PLASMID / COMPLEX (TRANSFERASE-INHIBITOR)
Function / homology
Function and homology information


Adenylate cyclase activating pathway / Hedgehog 'off' state / PKA activation / Adenylate cyclase inhibitory pathway / adenylate cyclase / cAMP biosynthetic process / G alpha (z) signalling events / adenylate cyclase activity / cAMP-mediated signaling / adenylate cyclase binding ...Adenylate cyclase activating pathway / Hedgehog 'off' state / PKA activation / Adenylate cyclase inhibitory pathway / adenylate cyclase / cAMP biosynthetic process / G alpha (z) signalling events / adenylate cyclase activity / cAMP-mediated signaling / adenylate cyclase binding / cellular response to forskolin / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / G-protein beta/gamma-subunit complex binding / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / adenylate cyclase-activating G protein-coupled receptor signaling pathway / manganese ion binding / membrane raft / dendrite / magnesium ion binding / protein-containing complex / ATP binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
Adenylate cyclase, conserved domain / Adenylate cyclase / Adenylate cyclase, N-terminal / Adenylate cyclase, conserved domain / Adenylyl cyclase N-terminal extracellular and transmembrane region / Nucleotide cyclase, GGDEF domain / Adenylyl cyclase class-4/guanylyl cyclase, conserved site / Guanylate cyclase signature. / Adenylyl- / guanylyl cyclase, catalytic domain / Adenylyl cyclase class-3/4/guanylyl cyclase ...Adenylate cyclase, conserved domain / Adenylate cyclase / Adenylate cyclase, N-terminal / Adenylate cyclase, conserved domain / Adenylyl cyclase N-terminal extracellular and transmembrane region / Nucleotide cyclase, GGDEF domain / Adenylyl cyclase class-4/guanylyl cyclase, conserved site / Guanylate cyclase signature. / Adenylyl- / guanylyl cyclase, catalytic domain / Adenylyl cyclase class-3/4/guanylyl cyclase / Adenylate and Guanylate cyclase catalytic domain / Guanylate cyclase domain profile. / Nucleotide cyclase / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FORSKOLIN / Adenylate cyclase type 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.2 Å
AuthorsZhang, G. / Hurley, J.H.
CitationJournal: Nature / Year: 1997
Title: Structure of the adenylyl cyclase catalytic core.
Authors: Zhang, G. / Liu, Y. / Ruoho, A.E. / Hurley, J.H.
History
DepositionFeb 4, 1997Processing site: BNL
Revision 1.0May 15, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ADENYLYL CYCLASE
B: ADENYLYL CYCLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7174
Polymers48,8962
Non-polymers8212
Water2,036113
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4970 Å2
ΔGint-20 kcal/mol
Surface area15280 Å2
MethodPISA
2
A: ADENYLYL CYCLASE
B: ADENYLYL CYCLASE
hetero molecules

A: ADENYLYL CYCLASE
B: ADENYLYL CYCLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,4338
Polymers97,7914
Non-polymers1,6424
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area12090 Å2
ΔGint-49 kcal/mol
Surface area28420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.300, 81.300, 180.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-94-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.198769, -0.978716, -0.051049), (-0.969057, 0.188495, 0.15937), (-0.146356, 0.081147, -0.985898)
Vector: 130.28723, 105.61935, -2.49822)

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Components

#1: Protein ADENYLYL CYCLASE /


Mass: 24447.781 Da / Num. of mol.: 2 / Fragment: C2 DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: PPROEX-1 / Plasmid: PPROEX-1 / Species (production host): Escherichia coli / Gene (production host): PPROEX-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: P26769, adenylate cyclase
#2: Chemical ChemComp-FOK / FORSKOLIN / Forskolin


Mass: 410.501 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H34O7
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 3 Å3/Da / Density % sol: 55 %
Crystal growpH: 5.9
Details: 1.1 M AM SO4, 0.1 M PHOSPHATE, PH 5.9, 2 % DMSO, 1 MM FORSKOLIN, 10 MM DTT, 80 MM NACL, 50 MM TRIS HCL
Crystal grow
*PLUS
Temperature: 21-24 ℃ / Method: unknown / PH range low: 5.9 / PH range high: 5.8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
117.5 mg/mlprotein11
21 mMforskolin12
32 %DMSO12
450 mMTris-HCl12
580 mM12NaCl
610 mMDTT12
71.1-1.2 Mammonium sulphate12
80.1 Msodium phophate12

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.908
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Dec 1, 1996
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.908 Å / Relative weight: 1
ReflectionResolution: 2.2→40 Å / Num. obs: 17326 / % possible obs: 91 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Net I/σ(I): 15
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 1 % / Mean I/σ(I) obs: 3 / % possible all: 40
Reflection
*PLUS
Num. measured all: 51618

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Processing

Software
NameVersionClassification
PHASESphasing
X-PLOR3.8model building
X-PLOR3.8refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.8phasing
RefinementMethod to determine structure: MIRAS / Resolution: 2.2→6 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 1.0E-5 / Isotropic thermal model: RESTRAINED / Cross valid method: FREE R / σ(F): 2 / Details: ANISOTROPIC DIFFRACTION
RfactorNum. reflection% reflectionSelection details
Rfree0.284 789 5 %RANDOM
Rwork0.219 ---
obs0.219 14696 54.2 %-
Displacement parametersBiso mean: 41 Å2
Refine analyzeLuzzati d res low obs: 6 Å
Refinement stepCycle: LAST / Resolution: 2.2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2764 0 58 113 2935
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.3
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINED
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPH19.PEP
X-RAY DIFFRACTION2FOR.PARTOPHCSDX.PRO
X-RAY DIFFRACTION3PARAM19.SOLFOR.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.3

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