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- PDB-3a7i: Human MST3 kinase in complex with adenine -

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Basic information

Entry
Database: PDB / ID: 3a7i
TitleHuman MST3 kinase in complex with adenine
ComponentsSerine/threonine kinase 24 (STE20 homolog, yeast)
KeywordsTRANSFERASE / two-lobe protein kinase fold / ATP-binding / Kinase / Nucleotide-binding
Function / homology
Function and homology information


Apoptotic execution phase / regulation of axon regeneration / execution phase of apoptosis / intrinsic apoptotic signaling pathway in response to oxidative stress / positive regulation of axon regeneration / Apoptotic cleavage of cellular proteins / cellular response to starvation / negative regulation of cell migration / response to hydrogen peroxide / protein autophosphorylation ...Apoptotic execution phase / regulation of axon regeneration / execution phase of apoptosis / intrinsic apoptotic signaling pathway in response to oxidative stress / positive regulation of axon regeneration / Apoptotic cleavage of cellular proteins / cellular response to starvation / negative regulation of cell migration / response to hydrogen peroxide / protein autophosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / cadherin binding / phosphorylation / Golgi membrane / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / nucleolus / Golgi apparatus / signal transduction / extracellular exosome / nucleoplasm / ATP binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Programmed cell death protein 10, dimerisation domain superfamily / : / Programmed cell death protein 10, dimerisation 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 ...Programmed cell death protein 10, dimerisation domain superfamily / : / Programmed cell death protein 10, dimerisation 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
ADENINE / non-specific serine/threonine protein kinase / Serine/threonine-protein kinase 24
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsKo, T.P. / Jeng, W.Y. / Liu, C.I. / Lai, M.D. / Wang, A.H.J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2010
Title: Structures of human MST3 kinase in complex with adenine, ADP and Mn2+.
Authors: Ko, T.P. / Jeng, W.Y. / Liu, C.I. / Lai, M.D. / Wu, C.L. / Chang, W.J. / Shr, H.L. / Lu, T.J. / Wang, A.H.J.
History
DepositionSep 26, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 4, 2012Group: Database references
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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 kinase 24 (STE20 homolog, yeast)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4712
Polymers34,3361
Non-polymers1351
Water7,512417
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.583, 55.598, 60.481
Angle α, β, γ (deg.)90.00, 111.13, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Serine/threonine kinase 24 (STE20 homolog, yeast) / MST3 kinase


Mass: 34336.191 Da / Num. of mol.: 1 / Fragment: N-terminal kinase domain (UNP RESIDUES 1-303)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STK24 / Plasmid: pET-32 Xa/LIC / Production host: Escherichia coli (E. coli) / Strain (production host): ArcticExpress(DE3) / References: UniProt: Q6P0Y1, UniProt: Q9Y6E0*PLUS
#2: Chemical ChemComp-ADE / ADENINE / Adenine


Mass: 135.127 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H5N5
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 417 / 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: 2.17 Å3/Da / Density % sol: 43.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 50mM Tris-HCl, 100mM NaCl, 10%(v/v) glycerol, 5mM dithiothreitol, 10mM ATP, 0.1M Tris-HCl, 200mM MgCl2, 13%(w/v) PEG 3350, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 23, 2007 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→30 Å / Num. all: 52288 / Num. obs: 50491 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 4.2 % / Rmerge(I) obs: 0.032 / Net I/σ(I): 45.7
Reflection shellResolution: 1.45→1.5 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.483 / Mean I/σ(I) obs: 2.6 / Num. unique all: 5083 / % possible all: 98.2

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3A7G

3a7g


Resolution: 1.45→30 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.217 2454 -random
Rwork0.187 ---
all0.194 52288 --
obs0.194 48955 93.6 %-
Displacement parametersBiso mean: 29 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.45→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2302 0 10 417 2729
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_bond_d0.019
LS refinement shellResolution: 1.45→1.5 Å / Rfactor Rfree error: 0.036
RfactorNum. reflection% reflection
Rfree0.312 223 -
Rwork0.276 --
obs-4382 84.4 %

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