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- PDB-8ak2: Drosophila melanogaster UNC89 Protein Kinase Domain 1 (apo) -

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Basic information

Entry
Database: PDB / ID: 8ak2
TitleDrosophila melanogaster UNC89 Protein Kinase Domain 1 (apo)
ComponentsObscurin
KeywordsSTRUCTURAL PROTEIN / Kinase / Muscle Protein
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 / Immunoglobulin subtype / Immunoglobulin / PH-like domain superfamily / 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
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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)35,79111
Polymers34,8101
Non-polymers98110
Water6,017334
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2540 Å2
ΔGint1 kcal/mol
Surface area13550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.424, 95.424, 164.767
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-3762-

HOH

21A-3799-

HOH

31A-3863-

HOH

41A-3897-

HOH

51A-3934-

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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 334 / 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: 3.2 Å3/Da / Density % sol: 61.56 %
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: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.75→29.21 Å / Num. obs: 45374 / % possible obs: 99.9 % / Redundancy: 13.12 % / Biso Wilson estimate: 28.88 Å2 / CC1/2: 0.999 / Net I/σ(I): 17.89
Reflection shellResolution: 1.75→1.77 Å / Num. unique obs: 1485 / CC1/2: 0.342

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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: 3GU4

3gu4


Resolution: 1.75→29.21 Å / SU ML: 0.2852 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.5683
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1959 2253 4.97 %
Rwork0.1738 43103 -
obs0.1749 45356 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.93 Å2
Refinement stepCycle: LAST / Resolution: 1.75→29.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2383 0 64 334 2781
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00732528
X-RAY DIFFRACTIONf_angle_d0.80853414
X-RAY DIFFRACTIONf_chiral_restr0.0556348
X-RAY DIFFRACTIONf_plane_restr0.0075438
X-RAY DIFFRACTIONf_dihedral_angle_d11.5665949
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.790.46351500.44532603X-RAY DIFFRACTION99.28
1.79-1.830.37811610.37882633X-RAY DIFFRACTION99.96
1.83-1.880.31871550.31172618X-RAY DIFFRACTION100
1.88-1.930.31611390.26212645X-RAY DIFFRACTION100
1.93-1.980.25431380.21182660X-RAY DIFFRACTION100
1.98-2.050.23431420.18522637X-RAY DIFFRACTION100
2.05-2.120.20471360.18942689X-RAY DIFFRACTION100
2.12-2.20.22831390.19822648X-RAY DIFFRACTION100
2.2-2.30.19561330.17132650X-RAY DIFFRACTION99.64
2.31-2.430.1831380.15862694X-RAY DIFFRACTION100
2.43-2.580.23311400.16872702X-RAY DIFFRACTION99.96
2.58-2.780.18691300.17122684X-RAY DIFFRACTION99.96
2.78-3.060.20651320.16632735X-RAY DIFFRACTION100
3.06-3.50.15521390.15172741X-RAY DIFFRACTION99.76
3.5-4.40.13461390.13062791X-RAY DIFFRACTION100
4.41-29.210.18911420.16892973X-RAY DIFFRACTION99.71

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