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- PDB-1cx4: CRYSTAL STRUCTURE OF A DELETION MUTANT OF THE TYPE II BETA REGULA... -

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Entry
Database: PDB / ID: 1cx4
TitleCRYSTAL STRUCTURE OF A DELETION MUTANT OF THE TYPE II BETA REGULATORY SUBUNIT OF CAMP-DEPENDENT PROTEIN KINASE
ComponentsCAMP-DEPENDENT PROTEIN KINASE REGULATORY SUBUNIT TYPE II BETACAMP-dependent pathway
KeywordsSIGNALING PROTEIN / BETA BARREL / CAMP-DEPENDENT PROTEIN KINASE / CAMP-BINDING / REGULATORY SUBUNIT
Function / homology
Function and homology information


GPER1 signaling / PKA activation in glucagon signalling / CREB1 phosphorylation through the activation of Adenylate Cyclase / DARPP-32 events / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 ...GPER1 signaling / PKA activation in glucagon signalling / CREB1 phosphorylation through the activation of Adenylate Cyclase / DARPP-32 events / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / Factors involved in megakaryocyte development and platelet production / Regulation of PLK1 Activity at G2/M Transition / Hedgehog 'off' state / PKA activation / response to antipsychotic drug / cAMP-dependent protein kinase regulator activity / Vasopressin regulates renal water homeostasis via Aquaporins / cAMP-dependent protein kinase inhibitor activity / ciliary base / cAMP-dependent protein kinase complex / protein kinase A catalytic subunit binding / cAMP binding / fatty acid metabolic process / dendritic shaft / learning / regulation of protein phosphorylation / modulation of chemical synaptic transmission / postsynapse / dendritic spine / protein domain specific binding / centrosome / dendrite / neuronal cell body / glutamatergic synapse / ubiquitin protein ligase binding / protein kinase binding / perinuclear region of cytoplasm / plasma membrane / cytosol / cytoplasm
Similarity search - Function
cAMP-dependent protein kinase regulatory subunit / cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain / Regulatory subunit of type II PKA R-subunit / RIIalpha, Regulatory subunit portion of type II PKA R-subunit / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. ...cAMP-dependent protein kinase regulatory subunit / cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain / Regulatory subunit of type II PKA R-subunit / RIIalpha, Regulatory subunit portion of type II PKA R-subunit / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / cAMP-dependent protein kinase type II-beta regulatory subunit
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.45 Å
AuthorsDiller, T.C. / Xuong, N.H. / Taylor, S.S.
Citation
Journal: Structure / Year: 2001
Title: Molecular basis for regulatory subunit diversity in cAMP-dependent protein kinase: crystal structure of the type II beta regulatory subunit.
Authors: Diller, T.C. / Madhusudan / Xuong, N.H. / Taylor, S.S.
#1: Journal: Protein Expr.Purif. / Year: 2000
Title: Type II beta regulatory subunit of cAMP-dependent protein kinase: purification strategies to optimize crystallization.
Authors: Diller, T.C. / Xuong, N.H. / Taylor, S.S.
History
DepositionAug 28, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_sheet.number_strands / _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: CAMP-DEPENDENT PROTEIN KINASE REGULATORY SUBUNIT TYPE II BETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8163
Polymers34,1581
Non-polymers6582
Water3,459192
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)161.620, 161.620, 39.660
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein CAMP-DEPENDENT PROTEIN KINASE REGULATORY SUBUNIT TYPE II BETA / CAMP-dependent pathway


Mass: 34157.719 Da / Num. of mol.: 1 / Fragment: CAMP BINDING DOMAINS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: INVITROGEN PRSET B / Production host: Escherichia coli (E. coli) / References: UniProt: P12369
#2: Chemical ChemComp-CMP / ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / CYCLIC AMP / CAMP / Cyclic adenosine monophosphate


Mass: 329.206 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H12N5O6P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 192 / 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: 4.38 Å3/Da / Density % sol: 70.8 %
Description: PROTEIN RESIDUES PRECEDING ARG 130 AND POSTERIOR TO VAL 413 IN THE AMINO ACID SEQUENCE ARE NOT INCLUDED IN THIS MODEL. ADDITIONALLY, LOOP REGION CONSISTING OF RESIDUES 326 LYS THROUGH ...Description: PROTEIN RESIDUES PRECEDING ARG 130 AND POSTERIOR TO VAL 413 IN THE AMINO ACID SEQUENCE ARE NOT INCLUDED IN THIS MODEL. ADDITIONALLY, LOOP REGION CONSISTING OF RESIDUES 326 LYS THROUGH 333 GLU WERE NOT TRACED IN ELECTRON DENSITY MAPS: NO PEPTIDE BOND EXISTS BETWEEN ARG 325 AND ASN 334 IN THIS STRUCTURAL MODEL.
Crystal growpH: 7.75 / Details: pH 7.75
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: Diller, T.C., (2000) Protein Expression Purif., 20, 357.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
126 mg/mlprotein1drop
280 mMTris1reservoirpH7.75
329 %PEG34001reservoir
480 mM1reservoirMgCl2

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Data collection

DiffractionMean temperature: 300.3 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 6, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.45→25 Å / Num. obs: 21965 / % possible obs: 98.7 % / Observed criterion σ(I): 0 / Redundancy: 4.182 % / Biso Wilson estimate: 36.4 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 14.3
Reflection shellResolution: 2.45→2.56 Å / Redundancy: 4 % / Rmerge(I) obs: 0.325 / Mean I/σ(I) obs: 3.94 / % possible all: 97.9
Reflection shell
*PLUS
% possible obs: 97.9 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS0.5refinement
RefinementResolution: 2.45→23 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
Details: INSUFFICIENT ELECTRON DENSITY EXISTED IN MAPS TO INCLUDE RESIDUE RANGES 112- 128, 326-333 AND 413-416.
RfactorNum. reflection% reflectionSelection details
Rfree0.198 2186 9.955 %RANDOM
Rwork0.176 ---
obs0.176 21958 98.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.37 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso mean: 43.6 Å2
Baniso -1Baniso -2Baniso -3
1-2.73 Å27.64 Å20 Å2
2--2.73 Å20 Å2
3----5.45 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.45→23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2163 0 44 192 2399
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.841.5
X-RAY DIFFRACTIONc_mcangle_it3.062
X-RAY DIFFRACTIONc_scbond_it3.172
X-RAY DIFFRACTIONc_scangle_it4.772.5
LS refinement shellResolution: 2.45→2.56 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2705 272 10.17 %
Rwork0.2461 2403 -
obs--97.95 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3CMP.PARAMCMP.TOP
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 23 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.76
X-RAY DIFFRACTIONc_mcbond_it1.84
X-RAY DIFFRACTIONc_scbond_it3.17
X-RAY DIFFRACTIONc_mcangle_it3.06
X-RAY DIFFRACTIONc_scangle_it4.77

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