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- PDB-1zrz: Crystal Structure of the Catalytic Domain of Atypical Protein Kin... -

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Basic information

Entry
Database: PDB / ID: 1zrz
TitleCrystal Structure of the Catalytic Domain of Atypical Protein Kinase C-iota
ComponentsProtein kinase C, iota
KeywordsTRANSFERASE / Protein-Inhibitor Complex / Structural Genomics / Structural Proteomics in Europe / SPINE
Function / homology
Function and homology information


Golgi vesicle budding / PAR polarity complex / Tight junction interactions / establishment of apical/basal cell polarity / protein kinase C / negative regulation of glial cell apoptotic process / diacylglycerol-dependent serine/threonine kinase activity / eye photoreceptor cell development / Schmidt-Lanterman incisure / cellular response to chemical stress ...Golgi vesicle budding / PAR polarity complex / Tight junction interactions / establishment of apical/basal cell polarity / protein kinase C / negative regulation of glial cell apoptotic process / diacylglycerol-dependent serine/threonine kinase activity / eye photoreceptor cell development / Schmidt-Lanterman incisure / cellular response to chemical stress / membrane organization / cell-cell junction organization / establishment or maintenance of epithelial cell apical/basal polarity / positive regulation of endothelial cell apoptotic process / tight junction / protein targeting to membrane / intercellular bridge / positive regulation of Notch signaling pathway / cell leading edge / regulation of postsynaptic membrane neurotransmitter receptor levels / brush border / bicellular tight junction / cytoskeleton organization / positive regulation of glial cell proliferation / vesicle-mediated transport / p75NTR recruits signalling complexes / response to interleukin-1 / secretion / actin filament organization / phospholipid binding / positive regulation of protein localization to plasma membrane / positive regulation of glucose import / Schaffer collateral - CA1 synapse / positive regulation of neuron projection development / Pre-NOTCH Transcription and Translation / cellular response to insulin stimulus / microtubule cytoskeleton / KEAP1-NFE2L2 pathway / cell migration / positive regulation of NF-kappaB transcription factor activity / negative regulation of neuron apoptotic process / endosome / protein kinase activity / intracellular signal transduction / apical plasma membrane / Golgi membrane / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / glutamatergic synapse / negative regulation of apoptotic process / extracellular exosome / nucleoplasm / ATP binding / metal ion binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Atypical protein kinase C iota type, catalytic domain / Protein kinase C / Protein kinase C, PB1 domain / PB1 domain / PB1 domain / PB1 domain profile. / PB1 domain / Protein kinase, C-terminal / Protein kinase C terminal domain / Diacylglycerol/phorbol-ester binding ...Atypical protein kinase C iota type, catalytic domain / Protein kinase C / Protein kinase C, PB1 domain / PB1 domain / PB1 domain / PB1 domain profile. / PB1 domain / Protein kinase, C-terminal / Protein kinase C terminal domain / Diacylglycerol/phorbol-ester binding / Phorbol esters/diacylglycerol binding domain (C1 domain) / Zinc finger phorbol-ester/DAG-type signature. / 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 / C1-like domain superfamily / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-BI1 / Protein kinase C iota type
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsMesserschmidt, A. / Macieira, S. / Velarde, M. / Baedeker, M. / Benda, C. / Jestel, A. / Brandstetter, H. / Neuefeind, T. / Blaesse, M. / Structural Proteomics in Europe (SPINE)
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Crystal Structure of the Catalytic Domain of Human Atypical Protein Kinase C-iota Reveals Interaction Mode of Phosphorylation Site in Turn Motif
Authors: Messerschmidt, A. / Macieira, S. / Velarde, M. / Baedeker, M. / Benda, C. / Jestel, A. / Brandstetter, H. / Neuefeind, T. / Blaesse, M.
History
DepositionMay 23, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 13, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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: Protein kinase C, iota
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4092
Polymers41,9961
Non-polymers4121
Water75742
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.143, 78.143, 112.625
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Protein kinase C, iota /


Mass: 41996.250 Da / Num. of mol.: 1 / Fragment: catalytic domain, residues 224-587
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRKCI / Plasmid: pFastBacHTa / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 cells
References: UniProt: P41743, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#2: Chemical ChemComp-BI1 / 3-{1-[3-(DIMETHYLAMINO)PROPYL]-1H-INDOL-3-YL}-4-(1H-INDOL-3-YL)-1H-PYRROLE-2,5-DIONE / RBT205 INHIBITOR / Bisindolylmaleimide


Mass: 412.484 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H24N4O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 2.48 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PEG 400, sodium acetate, MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.0003 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Aug 9, 2004 / Details: silicon monochromator
RadiationMonochromator: silicon monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0003 Å / Relative weight: 1
ReflectionResolution: 3→37 Å / Num. all: 8372 / Num. obs: 7778 / % possible obs: 92.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.7 % / Biso Wilson estimate: 59.9 Å2 / Rmerge(I) obs: 0.093 / Rsym value: 0.093 / Net I/σ(I): 6.5
Reflection shellResolution: 3→3.19 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.371 / Mean I/σ(I) obs: 2 / Num. unique all: 1183 / Rsym value: 0.371 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: protein kinase C-thate, PDB ENTRY 1XJD

1xjd


Resolution: 3→24.94 Å / Rfactor Rfree error: 0.017 / Data cutoff high absF: 3637087.06 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.333 394 5.2 %RANDOM
Rwork0.249 ---
obs0.249 7517 90.2 %-
all-8334 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.4917 Å2 / ksol: 0.319837 e/Å3
Displacement parametersBiso mean: 59.7 Å2
Baniso -1Baniso -2Baniso -3
1--9.08 Å25.95 Å20 Å2
2---9.08 Å20 Å2
3---18.17 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.58 Å0.44 Å
Luzzati d res low-6 Å
Luzzati sigma a0.61 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 3→24.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2450 0 31 42 2523
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_improper_angle_d0.89
X-RAY DIFFRACTIONc_mcbond_it1.491.5
X-RAY DIFFRACTIONc_mcangle_it2.582.5
X-RAY DIFFRACTIONc_scbond_it1.912
X-RAY DIFFRACTIONc_scangle_it3.053
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.049 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.401 68 5.1 %
Rwork0.287 1270 -
obs-1183 99.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4tpo.partpo.top
X-RAY DIFFRACTION5BI1.parBI1.top

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