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- PDB-8ak3: Drosophila melanogaster UNC89 Protein Kinase 1 in complex with ADP -

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Basic information

Entry
Database: PDB / ID: 8ak3
TitleDrosophila melanogaster UNC89 Protein Kinase 1 in complex with ADP
ComponentsObscurin
KeywordsSTRUCTURAL PROTEIN / Kinase / Muscle protein / ATP-binding
Function / homology
Function and homology information


adult somatic muscle development / protein localization to M-band / M band / sarcomere organization / tropomyosin binding / guanyl-nucleotide exchange factor activity / protein kinase binding / ATP binding
Similarity search - Function
: / SOS1/NGEF-like PH domain / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain ...: / SOS1/NGEF-like PH domain / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / PH-like domain superfamily / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Protein kinase domain / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Protein Obscurin
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsDorendorf, T. / Zacharchenko, T. / Mayans, O.
Funding support France, 1items
OrganizationGrant numberCountry
Human Frontier Science Program (HFSP)RGP0044/2012 France
CitationJournal: Open Biology / Year: 2023
Title: PK1 from Drosophila obscurin is an inactive pseudokinase with scaffolding properties.
Authors: Zacharchenko, T. / Dorendorf, T. / Locker, N. / Van Dijk, E. / Katzemich, A. / Diederichs, K. / Bullard, B. / Mayans, O.
History
DepositionJul 29, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 29, 2023Provider: repository / Type: Initial release
Revision 1.1May 10, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Feb 7, 2024Group: 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: Obscurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6987
Polymers34,8101
Non-polymers8886
Water3,873215
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-9 kcal/mol
Surface area13360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.418, 95.418, 164.600
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Space group name HallP6c2c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: x-y,-y,-z
#7: -x,-x+y,-z
#8: -x,-y,z+1/2
#9: y,x,-z
#10: -y,-x,-z+1/2
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-3715-

HOH

21A-3730-

HOH

31A-3813-

HOH

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Components

#1: Protein Obscurin / Muscle M-line assembly protein Unc-89


Mass: 34810.285 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Unc-89, CG33519 / Production host: Escherichia coli (E. coli)
References: UniProt: A8DYP0, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 3.11 Å3/Da / Density % sol: 60.41 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: 1M potassium sodium tartrate, 100 mM CHES pH 9.5, 200 mM lithium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.9→29.16 Å / Num. obs: 35642 / % possible obs: 100 % / Redundancy: 12.53 % / Biso Wilson estimate: 33.58 Å2 / CC1/2: 0.998 / Net I/σ(I): 14.83
Reflection shellResolution: 1.9→1.92 Å / Num. unique obs: 1080 / CC1/2: 0.312

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Processing

Software
NameVersionClassification
Cootmodel building
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8ak2

8ak2


Resolution: 1.9→29.16 Å / SU ML: 0.1956 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.143
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2078 1771 4.97 %
Rwork0.1735 33849 -
obs0.1752 35620 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.89 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2417 0 57 215 2689
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00812569
X-RAY DIFFRACTIONf_angle_d1.05293479
X-RAY DIFFRACTIONf_chiral_restr0.0603358
X-RAY DIFFRACTIONf_plane_restr0.0095446
X-RAY DIFFRACTIONf_dihedral_angle_d14.6039957
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.31971400.32642527X-RAY DIFFRACTION99.85
1.95-2.010.27591190.25182559X-RAY DIFFRACTION99.96
2.01-2.070.20841320.19662567X-RAY DIFFRACTION100
2.07-2.150.24971260.19172542X-RAY DIFFRACTION99.96
2.15-2.230.2161430.19382572X-RAY DIFFRACTION100
2.23-2.340.23641280.16672565X-RAY DIFFRACTION100
2.34-2.460.20851030.17752600X-RAY DIFFRACTION100
2.46-2.610.22041500.17992569X-RAY DIFFRACTION99.96
2.61-2.810.2341340.19382603X-RAY DIFFRACTION99.93
2.81-3.10.23351390.18642599X-RAY DIFFRACTION99.93
3.1-3.540.2091350.16542647X-RAY DIFFRACTION100
3.54-4.460.1741600.13992654X-RAY DIFFRACTION99.96
4.46-29.160.19011620.1662845X-RAY DIFFRACTION100

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