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- PDB-3dak: Crystal Structure of Domain-Swapped OSR1 kinase domain -

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Basic information

Entry
Database: PDB / ID: 3dak
TitleCrystal Structure of Domain-Swapped OSR1 kinase domain
ComponentsSerine/threonine-protein kinase OSR1
KeywordsTRANSFERASE / SERINE/THREONINE PROTEIN KINASE / STE20 / DOMAIN-SWAPPING / ATP-binding / Kinase / Magnesium / Metal-binding / Nucleotide-binding / Phosphoprotein / Polymorphism / Serine/threonine-protein kinase
Function / homology
Function and homology information


chemokine (C-C motif) ligand 21 signaling pathway / chemokine (C-X-C motif) ligand 12 signaling pathway / negative regulation of potassium ion transmembrane transport / renal sodium ion absorption / positive regulation of T cell chemotaxis / cellular hypotonic response / cellular response to chemokine / cellular hyperosmotic response / osmosensory signaling pathway / cell volume homeostasis ...chemokine (C-C motif) ligand 21 signaling pathway / chemokine (C-X-C motif) ligand 12 signaling pathway / negative regulation of potassium ion transmembrane transport / renal sodium ion absorption / positive regulation of T cell chemotaxis / cellular hypotonic response / cellular response to chemokine / cellular hyperosmotic response / osmosensory signaling pathway / cell volume homeostasis / peptidyl-threonine phosphorylation / response to oxidative stress / protein autophosphorylation / non-specific serine/threonine protein kinase / intracellular signal transduction / response to xenobiotic stimulus / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / protein kinase binding / magnesium ion binding / signal transduction / extracellular exosome / ATP binding / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Serine/threonine-protein kinase OSR1/WNK, CCT domain / Oxidative-stress-responsive kinase 1 C-terminal domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. ...Serine/threonine-protein kinase OSR1/WNK, CCT domain / Oxidative-stress-responsive kinase 1 C-terminal domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Serine/threonine-protein kinase OSR1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.25 Å
AuthorsLee, S. / Cobb, M.H. / Goldsmith, E.J.
CitationJournal: Protein Sci. / Year: 2008
Title: Crystal structure of domain-swapped STE20 OSR1 kinase domain.
Authors: Lee, S.J. / Cobb, M.H. / Goldsmith, E.J.
History
DepositionMay 29, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: Serine/threonine-protein kinase OSR1
B: Serine/threonine-protein kinase OSR1
C: Serine/threonine-protein kinase OSR1
D: Serine/threonine-protein kinase OSR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,83712
Polymers129,7154
Non-polymers2,1228
Water9,548530
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Serine/threonine-protein kinase OSR1
D: Serine/threonine-protein kinase OSR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,9186
Polymers64,8572
Non-polymers1,0614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5930 Å2
ΔGint-54 kcal/mol
Surface area26080 Å2
MethodPISA
3
B: Serine/threonine-protein kinase OSR1
C: Serine/threonine-protein kinase OSR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,9186
Polymers64,8572
Non-polymers1,0614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5820 Å2
ΔGint-53 kcal/mol
Surface area26190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.208, 104.484, 162.903
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Serine/threonine-protein kinase OSR1 / Oxidative stress-responsive 1 protein


Mass: 32428.639 Da / Num. of mol.: 4 / Fragment: Protein kinase domain, UNP residues 6-295
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Strain: 1-295 / Gene: OXSR1, KIAA1101, OSR1 / Plasmid: pHis-parallel vector / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA2(DE3)
References: UniProt: O95747, non-specific serine/threonine protein kinase
#2: Chemical
ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 530 / 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: 2.43 Å3/Da / Density % sol: 49.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 3350, Tri-Lithium Citrate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97899 Å
DetectorType: FLAT / Detector: CCD / Date: Jan 1, 2006 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97899 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 59432 / % possible obs: 98.2 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 9.5
Reflection shellResolution: 2.25→2.3 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.456 / % possible all: 92

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→30 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.912 / SU B: 13.91 / SU ML: 0.18 / Cross valid method: THROUGHOUT / ESU R Free: 0.252 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2671 3007 5.1 %RANDOM
Rwork0.19508 ---
obs0.19882 56330 98.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.636 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å20 Å20 Å2
2---0.45 Å20 Å2
3---0.7 Å2
Refinement stepCycle: LAST / Resolution: 2.25→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8776 0 128 530 9434
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0229091
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6651.99112297
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.40251115
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.61224.931363
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.742151670
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.2671533
X-RAY DIFFRACTIONr_chiral_restr0.1440.21374
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026603
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2170.24016
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.26123
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.2495
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2350.278
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2340.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.2931.55755
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.82328985
X-RAY DIFFRACTIONr_scbond_it3.82533835
X-RAY DIFFRACTIONr_scangle_it5.7634.53312
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.25→2.312 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 197 -
Rwork0.194 3755 -
obs--90.58 %

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