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- PDB-7lf3: C1B domain of Protein kinase C in complex with diacylglycerol-lac... -

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Basic information

Entry
Database: PDB / ID: 7lf3
TitleC1B domain of Protein kinase C in complex with diacylglycerol-lactone AJH-836
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 / apoptotic process / perinuclear region of cytoplasm / zinc ion binding / ATP binding / nucleus
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
Chem-XP5 / Chem-XZJ / Protein kinase C delta type
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.13 Å
AuthorsKatti, S.S. / Krieger, I.V.
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
DepositionJan 15, 2021Deposition 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

Downloads & links

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Assembly

Deposited unit
A: Protein kinase C delta type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,0935
Polymers6,0971
Non-polymers9964
Water1,11762
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR relaxation study
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4260 Å2
Unit cell
Length a, b, c (Å)34.913, 25.943, 57.642
Angle α, β, γ (deg.)90.000, 92.570, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-416-

HOH

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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: Chemical ChemComp-XZJ / {(2R,4E)-2-(hydroxymethyl)-4-[5-methyl-3-(2-methylpropyl)hexylidene]-5-oxooxolan-2-yl}methyl 2,2-dimethylpropanoate / AJH-836


Mass: 382.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H38O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-XP5 / (4S,7R)-7-(heptanoyloxy)-4-hydroxy-N,N,N-trimethyl-10-oxo-3,5,9-trioxa-4-phosphahexadecan-1-aminium 4-oxide


Mass: 482.568 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H45NO8P / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.14 Å3/Da / Density % sol: 42.48 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Screen condition: 0.2 M Ammonium acetate, 0.1 M Sodium Phosphate, 15% Isopropanol, pH 6.8; Drop condition: Protein: 2 mM in MES pH 6.5, 150 mM KCl, Phosphatidylcholine: 20 mM, AJH-836: 3 mM

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.00003 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 4, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 1.13→28.79 Å / Num. obs: 18593 / % possible obs: 95.6 % / Redundancy: 5.7 % / CC1/2: 0.975 / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.065 / Rrim(I) all: 0.145 / Net I/av σ(I): 15.5 / Net I/σ(I): 15.5
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
1.13-1.155.52.30446158420.3961.0632.5470.686.6
6.19-28.7950.0536561320.9880.0280.0642.697

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Processing

Software
NameVersionClassification
XDSdata 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: 1.13→28.79 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1993 1884 10.15 %
Rwork0.1826 16678 -
obs0.1844 18562 94.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 169.09 Å2 / Biso mean: 24.4154 Å2 / Biso min: 12.05 Å2
Refinement stepCycle: final / Resolution: 1.13→28.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms417 0 51 62 530
Biso mean--46.4 32.43 -
Num. residues----52
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006504
X-RAY DIFFRACTIONf_angle_d0.942687
X-RAY DIFFRACTIONf_dihedral_angle_d19.89287
X-RAY DIFFRACTIONf_chiral_restr0.07971
X-RAY DIFFRACTIONf_plane_restr0.00783
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.13-1.160.47941270.46551155128287
1.16-1.190.39191440.37061247139193
1.19-1.230.29331330.29751247138093
1.23-1.280.31461530.27581269142294
1.28-1.330.27211410.23871246138794
1.33-1.390.24851460.21051273141995
1.39-1.460.20821340.20771296143095
1.46-1.550.20551480.18621306145496
1.55-1.670.20041490.17211280142996
1.67-1.840.17211400.17291317145797
1.84-2.110.17121510.16331308145997
2.11-2.660.17411550.17211349150498
2.66-28.790.19441630.16461385154899

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