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- PDB-4l0n: Crystal structure of STK3 (MST2) SARAH domain -

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Basic information

Entry
Database: PDB / ID: 4l0n
TitleCrystal structure of STK3 (MST2) SARAH domain
ComponentsSerine/threonine-protein kinase 3
KeywordsTRANSFERASE / Structural Genomics / Structural Genomics Consortium / SGC / SARAH domain / STK3 / MST2 / heptad repeat / structural genomics consortium (SGC)
Function / homology
Function and homology information


regulation of cell differentiation involved in embryonic placenta development / cell differentiation involved in embryonic placenta development / primitive hemopoiesis / neural tube formation / positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of hippo signaling / endocardium development / negative regulation of organ growth / hippo signaling / transcription regulator activator activity ...regulation of cell differentiation involved in embryonic placenta development / cell differentiation involved in embryonic placenta development / primitive hemopoiesis / neural tube formation / positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of hippo signaling / endocardium development / negative regulation of organ growth / hippo signaling / transcription regulator activator activity / Signaling by Hippo / protein localization to centrosome / organ growth / hepatocyte apoptotic process / regulation of MAPK cascade / extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of fat cell differentiation / canonical Wnt signaling pathway / JNK cascade / protein serine/threonine kinase activator activity / central nervous system development / epithelial cell proliferation / phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein tetramerization / positive regulation of JNK cascade / negative regulation of canonical Wnt signaling pathway / protein import into nucleus / negative regulation of epithelial cell proliferation / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / non-specific serine/threonine protein kinase / protein kinase activity / protein stabilization / intracellular signal transduction / protein phosphorylation / positive regulation of apoptotic process / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / centrosome / magnesium ion binding / protein-containing complex / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / Mst1 SARAH domain / C terminal SARAH domain of Mst1 / SARAH domain / SARAH domain profile. / p53, subunit A / p53-like tetramerisation domain / : / p53-like tetramerisation domain superfamily / Few Secondary Structures ...: / Mst1 SARAH domain / C terminal SARAH domain of Mst1 / SARAH domain / SARAH domain profile. / p53, subunit A / p53-like tetramerisation domain / : / p53-like tetramerisation domain superfamily / Few Secondary Structures / Irregular / 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
Serine/threonine-protein kinase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.4 Å
AuthorsChaikuad, A. / Krojer, T. / Newman, J.A. / Dixon-Clarke, S. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of STK3 (MST2) SARAH domain
Authors: Chaikuad, A. / Krojer, T. / Newman, J.A. / Dixon-Clarke, S. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Knapp, S. / Structural Genomics Consortium (SGC)
History
DepositionMay 31, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein kinase 3
B: Serine/threonine-protein kinase 3
C: Serine/threonine-protein kinase 3
D: Serine/threonine-protein kinase 3
E: Serine/threonine-protein kinase 3
F: Serine/threonine-protein kinase 3
G: Serine/threonine-protein kinase 3
H: Serine/threonine-protein kinase 3
I: Serine/threonine-protein kinase 3
J: Serine/threonine-protein kinase 3


Theoretical massNumber of molelcules
Total (without water)61,68210
Polymers61,68210
Non-polymers00
Water14,394799
1
A: Serine/threonine-protein kinase 3
B: Serine/threonine-protein kinase 3


Theoretical massNumber of molelcules
Total (without water)12,3362
Polymers12,3362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2820 Å2
ΔGint-31 kcal/mol
Surface area7450 Å2
MethodPISA
2
C: Serine/threonine-protein kinase 3
D: Serine/threonine-protein kinase 3


Theoretical massNumber of molelcules
Total (without water)12,3362
Polymers12,3362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2900 Å2
ΔGint-31 kcal/mol
Surface area7390 Å2
MethodPISA
3
E: Serine/threonine-protein kinase 3
F: Serine/threonine-protein kinase 3


Theoretical massNumber of molelcules
Total (without water)12,3362
Polymers12,3362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2760 Å2
ΔGint-31 kcal/mol
Surface area7600 Å2
MethodPISA
4
G: Serine/threonine-protein kinase 3
H: Serine/threonine-protein kinase 3


Theoretical massNumber of molelcules
Total (without water)12,3362
Polymers12,3362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2830 Å2
ΔGint-28 kcal/mol
Surface area7670 Å2
MethodPISA
5
I: Serine/threonine-protein kinase 3

I: Serine/threonine-protein kinase 3


Theoretical massNumber of molelcules
Total (without water)12,3362
Polymers12,3362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area2580 Å2
ΔGint-27 kcal/mol
Surface area7940 Å2
MethodPISA
6
J: Serine/threonine-protein kinase 3

J: Serine/threonine-protein kinase 3


Theoretical massNumber of molelcules
Total (without water)12,3362
Polymers12,3362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area2450 Å2
ΔGint-27 kcal/mol
Surface area7390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.320, 61.320, 301.860
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11C-548-

HOH

21C-565-

HOH

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Components

#1: Protein
Serine/threonine-protein kinase 3 / Mammalian STE20-like protein kinase 2 / MST-2 / STE20-like kinase MST2 / Serine/threonine-protein ...Mammalian STE20-like protein kinase 2 / MST-2 / STE20-like kinase MST2 / Serine/threonine-protein kinase Krs-1 / Serine/threonine-protein kinase 3 36kDa subunit / MST2/N / Serine/threonine-protein kinase 3 20kDa subunit / MST2/C


Mass: 6168.191 Da / Num. of mol.: 10 / Fragment: SARAH domain (UNP residues 436-484)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KRS1, MST2, STK3 / Plasmid: pNIC28-BSA4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3
References: UniProt: Q13188, non-specific serine/threonine protein kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 799 / 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: 2.3 Å3/Da / Density % sol: 46.53 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 4.9
Details: 30% MPD, 0.1M acetate pH 4.9, 0.2M calcium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 19, 2013
RadiationMonochromator: Si (111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.4→32.84 Å / Num. all: 114405 / Num. obs: 114371 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 12.9
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 5 % / Rmerge(I) obs: 0.544 / Mean I/σ(I) obs: 2.9 / % possible all: 99.8

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Processing

Software
NameVersionClassification
GDAdata collection
SHARPphasing
REFMAC5.7.0032refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.4→30.66 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.284 / SU ML: 0.041 / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20667 5733 5 %RANDOM
Rwork0.16043 ---
obs0.16279 108637 99.54 %-
all-114371 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.17 Å2
Baniso -1Baniso -2Baniso -3
1-0.46 Å2-0 Å20 Å2
2--0.46 Å2-0 Å2
3----0.91 Å2
Refine analyzeLuzzati coordinate error obs: 0.189 Å
Refinement stepCycle: LAST / Resolution: 1.4→30.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4225 0 0 799 5024
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0194572
X-RAY DIFFRACTIONr_bond_other_d0.0010.024632
X-RAY DIFFRACTIONr_angle_refined_deg1.7182.0256142
X-RAY DIFFRACTIONr_angle_other_deg0.805310724
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7735573
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.37524245
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.654151036
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5631558
X-RAY DIFFRACTIONr_chiral_restr0.0950.2667
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025065
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02981
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.6381.7852118
X-RAY DIFFRACTIONr_mcbond_other2.6381.7852117
X-RAY DIFFRACTIONr_mcangle_it3.0982.6732648
X-RAY DIFFRACTIONr_scbond_it3.8772.2312454
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr4.88339204
X-RAY DIFFRACTIONr_sphericity_free30.995237
X-RAY DIFFRACTIONr_sphericity_bonded10.76159687
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 422 -
Rwork0.204 7849 -
obs--99.57 %

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