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- PDB-1s0p: Structure of the N-Terminal Domain of the Adenylyl Cyclase-Associ... -

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Basic information

Entry
Database: PDB / ID: 1s0p
TitleStructure of the N-Terminal Domain of the Adenylyl Cyclase-Associated Protein (CAP) from Dictyostelium discoideum.
ComponentsAdenylyl cyclase-associated protein
KeywordsMEMBRANE PROTEIN / Alpha helix bundle
Function / homology
Function and homology information


slug development involved in sorocarp development / macropinosome / pinocytosis / contractile vacuole organization / Neutrophil degranulation / aggregation involved in sorocarp development / response to osmotic stress / vacuolar membrane / establishment or maintenance of cell polarity / pseudopodium ...slug development involved in sorocarp development / macropinosome / pinocytosis / contractile vacuole organization / Neutrophil degranulation / aggregation involved in sorocarp development / response to osmotic stress / vacuolar membrane / establishment or maintenance of cell polarity / pseudopodium / mitotic cytokinesis / adenylate cyclase binding / : / phagocytic cup / extracellular matrix / actin filament organization / cell-cell adhesion / phagocytic vesicle membrane / actin binding / regulation of gene expression / cell cortex / vesicle / cytoplasm
Similarity search - Function
Adenylate cyclase-associated CAP, N-terminal domain / Adenylate cyclase-associated CAP, N-terminal / CAP, conserved site, N-terminal / CAP, conserved site, C-terminal / Adenylate cyclase-associated CAP, N-terminal domain superfamily / : / CAP N-terminal conserved motif / CAP, N-terminal domain / CAP protein signature 1. / CAP protein signature 2. ...Adenylate cyclase-associated CAP, N-terminal domain / Adenylate cyclase-associated CAP, N-terminal / CAP, conserved site, N-terminal / CAP, conserved site, C-terminal / Adenylate cyclase-associated CAP, N-terminal domain superfamily / : / CAP N-terminal conserved motif / CAP, N-terminal domain / CAP protein signature 1. / CAP protein signature 2. / Adenylate cyclase-associated CAP / Adenylate cyclase-associated CAP, C-terminal / Adenylate cyclase associated (CAP) C terminal / Adenylate cyclase-associated CAP, C-terminal superfamily / CARP motif / Domain in CAPs (cyclase-associated proteins) and X-linked retinitis pigmentosa 2 gene product. / C-CAP/cofactor C-like domain / C-CAP/cofactor C-like domain profile. / Cyclase-associated protein CAP/septum formation inhibitor MinC, C-terminal / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
Adenylyl cyclase-associated protein
Similarity search - Component
Biological speciesDictyostelium discoideum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.4 Å
AuthorsKsiazek, D. / Brandstetter, H. / Israel, L. / Bourenkov, G.P. / Katchalova, G. / Janssen, K.P. / Bartunik, H.D. / Noegel, A.A. / Schleicher, M. / Holak, T.A.
CitationJournal: Structure / Year: 2003
Title: STRUCTURE OF THE N-TERMINAL DOMAIN OF THE ADENYLYL CYCLASE-ASSOCIATED PROTEIN (CAP) FROM DICTYOSTELIUM DISCOIDEUM
Authors: Ksiazek, D. / Brandstetter, H. / Israel, L. / Bourenkov, G.P. / Katchalova, G. / Janssen, K.P. / Bartunik, H.D. / Noegel, A.A. / Schleicher, M. / Holak, T.A.
History
DepositionJan 1, 2004Deposition site: RCSB / Processing site: RCSB
SupersessionJan 27, 2004ID: 1PN1
Revision 1.0Jan 27, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _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

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Assembly

Deposited unit
A: Adenylyl cyclase-associated protein
B: Adenylyl cyclase-associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3813
Polymers39,3562
Non-polymers241
Water10,773598
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.52, 42.13, 53.74
Angle α, β, γ (deg.)97.42, 105.09, 97.15
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Adenylyl cyclase-associated protein / CAP


Mass: 19678.219 Da / Num. of mol.: 2 / Fragment: N-terminal domain (residues 51-226)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dictyostelium discoideum (eukaryote) / Gene: CAP / Production host: Escherichia coli (E. coli) / References: UniProt: P54654
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 598 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.63 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: 30% PEG8000, 0.2 M MgCl2, 10 mM -mercaptoethanol, and 0.1 M MES, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
130 %PEG80001reservoir
20.2 M1reservoirMgCl2
310 mMbeta-mercaptoethanol1reservoir
40.1 MMES1reservoirpH6.1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 0.9760, 0.9176, 1.105
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Apr 30, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9761
20.91761
31.1051
ReflectionResolution: 1.4→1.8 Å / Num. all: 58737 / Num. obs: 20092 / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.4→1.8 Å
Reflection
*PLUS
Lowest resolution: 20 Å / Num. obs: 58737 / % possible obs: 93.7 % / Num. measured all: 3602228 / Rmerge(I) obs: 0.032
Reflection shell
*PLUS
Highest resolution: 1.4 Å / Lowest resolution: 1.42 Å / % possible obs: 92.9 % / Rmerge(I) obs: 0.128 / Mean I/σ(I) obs: 4.6

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.4→1.8 Å / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection
Rfree0.21 -
Rwork0.18 -
all0.27 58737
obs0.26 20092
Refinement stepCycle: LAST / Resolution: 1.4→1.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2780 0 1 598 3379
Refinement
*PLUS
Lowest resolution: 20 Å / Num. reflection obs: 3602228 / Rfactor Rwork: 0.184
Solvent computation
*PLUS
Displacement parameters
*PLUS

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