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- PDB-1a25: C2 DOMAIN FROM PROTEIN KINASE C (BETA) -

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Basic information

Entry
Database: PDB / ID: 1a25
TitleC2 DOMAIN FROM PROTEIN KINASE C (BETA)
ComponentsPROTEIN KINASE C (BETA)
KeywordsCALCIUM-BINDING PROTEIN / CALCIUM++/PHOSPHOLIPID BINDING PROTEIN
Function / homology
Function and homology information


dibenzo-p-dioxin metabolic process / Depolymerization of the Nuclear Lamina / Disinhibition of SNARE formation / Response to elevated platelet cytosolic Ca2+ / Activation of NF-kappaB in B cells / cellular response to carbohydrate stimulus / VEGFR2 mediated cell proliferation / calcium,diacylglycerol-dependent serine/threonine kinase activity / positive regulation of odontogenesis of dentin-containing tooth / protein kinase C signaling ...dibenzo-p-dioxin metabolic process / Depolymerization of the Nuclear Lamina / Disinhibition of SNARE formation / Response to elevated platelet cytosolic Ca2+ / Activation of NF-kappaB in B cells / cellular response to carbohydrate stimulus / VEGFR2 mediated cell proliferation / calcium,diacylglycerol-dependent serine/threonine kinase activity / positive regulation of odontogenesis of dentin-containing tooth / protein kinase C signaling / histone H3T6 kinase activity / spectrin / regulation of D-glucose transmembrane transport / WNT5A-dependent internalization of FZD4 / RHO GTPases Activate NADPH Oxidases / negative regulation of D-glucose transmembrane transport / protein kinase C / phospholipase C-activating G protein-coupled acetylcholine receptor signaling pathway / diacylglycerol-dependent serine/threonine kinase activity / response to angiotensin / regulation of growth / positive regulation of vascular endothelial growth factor receptor signaling pathway / response to vitamin D / nuclear androgen receptor binding / regulation of synaptic vesicle exocytosis / Trafficking of GluR2-containing AMPA receptors / regulation of dopamine secretion / B cell activation / response to glucose / presynaptic cytosol / presynaptic modulation of chemical synaptic transmission / negative regulation of insulin receptor signaling pathway / protein kinase C binding / calyx of Held / B cell receptor signaling pathway / calcium channel regulator activity / brush border membrane / positive regulation of insulin secretion / positive regulation of angiogenesis / intracellular calcium ion homeostasis / calcium ion transport / response to ethanol / histone binding / adaptive immune response / transcription coactivator activity / positive regulation of canonical NF-kappaB signal transduction / intracellular signal transduction / response to xenobiotic stimulus / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / centrosome / chromatin binding / regulation of transcription by RNA polymerase II / zinc ion binding / ATP binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Classical protein kinase C beta, catalytic domain / Protein kinase C, alpha/beta/gamma types / Protein kinase, C-terminal / Protein kinase C terminal domain / Diacylglycerol/phorbol-ester binding / Phorbol esters/diacylglycerol binding domain (C1 domain) / C2 domain / Zinc finger phorbol-ester/DAG-type signature. / Protein kinase C conserved region 2 (CalB) / C2 domain ...Classical protein kinase C beta, catalytic domain / Protein kinase C, alpha/beta/gamma types / Protein kinase, C-terminal / Protein kinase C terminal domain / Diacylglycerol/phorbol-ester binding / Phorbol esters/diacylglycerol binding domain (C1 domain) / C2 domain / Zinc finger phorbol-ester/DAG-type signature. / Protein kinase C conserved region 2 (CalB) / C2 domain / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / C2 domain / C2 domain profile. / C1-like domain superfamily / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / C2 domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
O-PHOSPHOETHANOLAMINE / Protein kinase C beta type
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsSutton, R.B. / Sprang, S.R.
CitationJournal: Structure / Year: 1998
Title: Structure of the protein kinase Cbeta phospholipid-binding C2 domain complexed with Ca2+.
Authors: Sutton, R.B. / Sprang, S.R.
History
DepositionJan 16, 1998Processing site: BNL
Revision 1.0May 6, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN KINASE C (BETA)
B: PROTEIN KINASE C (BETA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1769
Polymers33,7642
Non-polymers4127
Water88349
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2460 Å2
ΔGint-77 kcal/mol
Surface area13200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.798, 77.798, 140.826
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.912012, 0.409902, -0.014639), (0.410099, 0.910658, -0.050199), (-0.007246, -0.051786, -0.998632)
Vector: -16.5808, 4.693, 41.7363)

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Components

#1: Protein PROTEIN KINASE C (BETA) / CALB


Mass: 16882.111 Da / Num. of mol.: 2 / Fragment: CALCIUM/PHOSPHOLIPID BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Cell line: BL21 / Plasmid: PGEX-KG / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)
References: UniProt: P68403, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-PSE / O-PHOSPHOETHANOLAMINE


Mass: 171.089 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H10NO5P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.5 Å3/Da / Density % sol: 64 %
Crystal growpH: 6.5
Details: PROTEIN WAS CRYSTALLIZED FROM 15% PEG1500, 100 MM MES, PH 6.5
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 21 ℃ / pH: 6.4 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 %(w/v)PEG15001drop
22 mM1dropCaCl2
32 mMo-phospho-L-serine1drop
4100 mMMES1drop

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Data collection

DiffractionMean temperature: 133 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.918
DetectorType: PRINCETON 2K / Detector: CCD / Date: Oct 1, 1996 / Details: MIRRORS
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.7→40 Å / Num. obs: 12297 / % possible obs: 98.5 % / Observed criterion σ(I): 2 / Redundancy: 8.9 % / Biso Wilson estimate: 50.7 Å2 / Rmerge(I) obs: 0.136 / Rsym value: 0.083 / Net I/σ(I): 13
Reflection shellResolution: 2.7→2.9 Å / Redundancy: 5 % / Rmerge(I) obs: 0.13 / Mean I/σ(I) obs: 8 / Rsym value: 0.26 / % possible all: 95

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.2refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RSY

1rsy


Resolution: 2.7→20 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1365552.04 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: REFINEMENT TARGET FUNCTION : MLF DATA CUTOFF HIGH (ABS(F)) : 1365552.04 DATA CUTOFF LOW (ABS(F)) : 0.000000
RfactorNum. reflection% reflectionSelection details
Rfree0.254 1254 10.3 %RANDOM
Rwork0.222 ---
obs0.222 12233 98.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 25 Å2 / ksol: 0.345 e/Å3
Displacement parametersBiso mean: 40.7 Å2
Baniso -1Baniso -2Baniso -3
1--3.61 Å20 Å20 Å2
2---3.61 Å20 Å2
3---7.22 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2176 0 16 49 2241
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
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_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.371.5
X-RAY DIFFRACTIONc_mcangle_it5.222
X-RAY DIFFRACTIONc_scbond_it5.832
X-RAY DIFFRACTIONc_scangle_it8.042.5
Refine LS restraints NCSNCS model details: CONSTRAINED
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.422 182 9.4 %
Rwork0.355 1759 -
obs--96.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2PSE.PARPSE.TOP
X-RAY DIFFRACTION3PARCAL.PROTOPCAL.PRO
X-RAY DIFFRACTION4WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 0.2 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.77

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