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- PDB-7knd: C1B domain of Protein kinase C in apo form -

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Basic information

Entry
Database: PDB / ID: 7knd
TitleC1B domain of Protein kinase C in apo form
ComponentsProtein kinase C delta type
KeywordsLIPID BINDING PROTEIN / C1 / lipid-binding / diacylglycerol-binding / Zn2+ finger
Function / homology
Function and homology information


protein kinase C / diacylglycerol-dependent serine/threonine kinase activity / response to glucose / intracellular signal transduction / apoptotic process / perinuclear region of cytoplasm / zinc ion binding / ATP binding / nucleus / plasma membrane
Similarity search - Function
Protein kinase C, delta / 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. / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) ...Protein kinase C, delta / 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. / 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
Similarity search - Domain/homology
Protein kinase C delta type
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.39 Å
AuthorsKatti, S.S. / Krieger, I.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM108998 United States
CitationJournal: Nat Commun / Year: 2022
Title: Structural anatomy of Protein Kinase C C1 domain interactions with diacylglycerol and other agonists.
Authors: Katti, S.S. / Krieger, I.V. / Ann, J. / Lee, J. / Sacchettini, J.C. / Igumenova, T.I.
History
DepositionNov 4, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein kinase C delta type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,2283
Polymers6,0971
Non-polymers1312
Water46826
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, NMR relaxation study
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area3980 Å2
Unit cell
Length a, b, c (Å)37.264, 37.264, 31.888
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Protein kinase C delta type / nPKC-delta


Mass: 6097.217 Da / Num. of mol.: 1 / Fragment: C1B domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Prkcd, rCG_42255 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A140UHX0
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.82 Å3/Da / Density % sol: 32.25 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Screen: 0.2 M Ammonium acetate, 0.1 M Sodium phosphate, 30% Isopropanol, pH 6.8, Drop condition: Protein: 1.2 mM in MES pH 6.5, 150 mM KCl

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER X8 PROTEUM / Wavelength: 1.54 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: Jul 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.39→37.26 Å / Num. obs: 8924 / % possible obs: 100 % / Redundancy: 6.3 % / CC1/2: 0.995 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.025 / Rrim(I) all: 0.062 / Net I/σ(I): 15 / Num. measured all: 56048 / Scaling rejects: 6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.39-1.414.31.65918314300.5220.9051.8950.8100
7.61-37.266.10.051389640.9930.0230.05642.499.5

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Processing

Software
NameVersionClassification
SAINTdata reduction
Aimless0.7.4data scaling
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ptq

1ptq


Resolution: 1.39→37.26 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 40.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2464 881 9.9 %
Rwork0.2165 8016 -
obs0.2196 8897 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 61.55 Å2 / Biso mean: 31.9641 Å2 / Biso min: 17.2 Å2
Refinement stepCycle: final / Resolution: 1.39→37.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms417 0 2 26 445
Biso mean--25.95 33.33 -
Num. residues----52
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009434
X-RAY DIFFRACTIONf_angle_d1.354583
X-RAY DIFFRACTIONf_dihedral_angle_d8.21958
X-RAY DIFFRACTIONf_chiral_restr0.159
X-RAY DIFFRACTIONf_plane_restr0.00974
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.39-1.480.36411460.332913151461
1.48-1.590.30291480.256913241472
1.59-1.750.26981470.2813271474
1.75-20.26221420.265213301472
2-2.520.26361440.241713461490
2.53-37.260.22511540.180413741528

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