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- PDB-1xjd: Crystal Structure of PKC-theta complexed with Staurosporine at 2A... -

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Basic information

Entry
Database: PDB / ID: 1xjd
TitleCrystal Structure of PKC-theta complexed with Staurosporine at 2A resolution
ComponentsProtein kinase C, theta type
KeywordsTRANSFERASE / KINASE / PKC-theta / ATP / AMP
Function / homology
Function and homology information


positive regulation of T-helper 2 cell activation / protein kinase C / Netrin-1 signaling / diacylglycerol-dependent serine/threonine kinase activity / CD4-positive, alpha-beta T cell proliferation / Effects of PIP2 hydrolysis / regulation of platelet aggregation / positive regulation of CD4-positive, alpha-beta T cell proliferation / negative regulation of T cell apoptotic process / positive regulation of T-helper 17 type immune response ...positive regulation of T-helper 2 cell activation / protein kinase C / Netrin-1 signaling / diacylglycerol-dependent serine/threonine kinase activity / CD4-positive, alpha-beta T cell proliferation / Effects of PIP2 hydrolysis / regulation of platelet aggregation / positive regulation of CD4-positive, alpha-beta T cell proliferation / negative regulation of T cell apoptotic process / positive regulation of T-helper 17 type immune response / aggresome / Apoptotic cleavage of cellular proteins / positive regulation of interleukin-17 production / Fc-epsilon receptor signaling pathway / positive regulation of telomere capping / membrane protein ectodomain proteolysis / immunological synapse / centriolar satellite / positive regulation of interleukin-4 production / negative regulation of insulin receptor signaling pathway / positive regulation of telomerase activity / positive regulation of telomere maintenance via telomerase / positive regulation of interleukin-2 production / cell chemotaxis / axon guidance / regulation of cell growth / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / G alpha (z) signalling events / FCERI mediated NF-kB activation / RAS processing / Inactivation, recovery and regulation of the phototransduction cascade / positive regulation of T cell activation / Downstream TCR signaling / positive regulation of NF-kappaB transcription factor activity / protein kinase activity / intracellular signal transduction / inflammatory response / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / regulation of DNA-templated transcription / ATP binding / metal ion binding / plasma membrane / cytosol
Similarity search - Function
Protein kinase C, theta / Novel protein kinase C theta, catalytic domain / Protein kinase C delta/epsilon/eta/theta, C2 domain / Protein kinase C, delta/epsilon/eta/theta types / 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. / C2 domain ...Protein kinase C, theta / Novel protein kinase C theta, catalytic domain / Protein kinase C delta/epsilon/eta/theta, C2 domain / Protein kinase C, delta/epsilon/eta/theta types / 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. / C2 domain / C2 domain profile. / 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. / C2 domain superfamily / 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
STAUROSPORINE / Protein kinase C theta type
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsXu, Z.B.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Catalytic domain crystal structure of protein kinase C-theta (PKCtheta)
Authors: Xu, Z.B. / Chaudhary, D. / Olland, S. / Wolfrom, S. / Czerwinski, R. / Malakian, K. / Lin, L. / Stahl, M.L. / Joseph-McCarthy, D. / Benander, C. / Fitz, L. / Greco, R. / Somers, W.S. / Mosyak, L.
History
DepositionSep 23, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2004Provider: 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

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Assembly

Deposited unit
A: Protein kinase C, theta type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2892
Polymers40,8221
Non-polymers4671
Water2,072115
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)139.566, 42.400, 67.678
Angle α, β, γ (deg.)90.00, 116.24, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Protein kinase C, theta type / / PKC-theta / nPKC-theta


Mass: 40822.016 Da / Num. of mol.: 1
Fragment: residues 362-706: includes Protein Kinase Domain (residues 380-634)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Description: THE SEQUENCE OF THIS PEPTIDE CAN BE FOUND NATURALLY IN HOMO SAPIENS (HUMAN).
Gene: PKC / Plasmid: PET16B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3
References: UniProt: Q04759, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#2: Chemical ChemComp-STU / STAUROSPORINE / Staurosporine


Mass: 466.531 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H26N4O3 / Comment: anticancer, antifungal, antibiotic, alkaloid*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 2.19 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 2M Ammonium Sulfate, 40mM DTT, 0.1M bis-tris, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 17, 2003
RadiationMonochromator: yes / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 24428 / Num. obs: 23134 / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.33 % / Biso Wilson estimate: 10.9 Å2 / Rmerge(I) obs: 0.058 / Rsym value: 0.041 / Net I/σ(I): 19.3
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.11 % / Rmerge(I) obs: 0.276 / Mean I/σ(I) obs: 2.5 / Rsym value: 0.236 / % possible all: 63.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1STC

1stc


Resolution: 2→19.93 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 144989.1 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.216 818 4 %RANDOM
Rwork0.201 ---
obs0.201 20257 83.2 %-
all-24317 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 60.8563 Å2 / ksol: 0.432303 e/Å3
Displacement parametersBiso mean: 29 Å2
Baniso -1Baniso -2Baniso -3
1--4.51 Å20 Å2-3.43 Å2
2--4.82 Å20 Å2
3----0.31 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2→19.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2352 0 35 115 2502
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.11.5
X-RAY DIFFRACTIONc_mcangle_it1.812
X-RAY DIFFRACTIONc_scbond_it1.82
X-RAY DIFFRACTIONc_scangle_it2.712.5
LS refinement shellResolution: 2→2.13 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rwork0.239 2008 -
obs--50 %
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 DIFFRACTION4STU.PARAMSTU.TOP

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