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- PDB-8a66: Crystal structure of MST2 in complex with XMU-MP-1 -

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Entry
Database: PDB / ID: 8a66
TitleCrystal structure of MST2 in complex with XMU-MP-1
Components(Serine/threonine-protein kinase 3 36kDa subunit) x 2
KeywordsTRANSCRIPTION / Serine/threonine kinase / autophosrylation / transferase
Function / homology
Function and homology information


cell differentiation involved in embryonic placenta development / regulation of cell differentiation involved in embryonic placenta development / primitive hemopoiesis / neural tube formation / positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / endocardium development / negative regulation of organ growth / hippo signaling / Signaling by Hippo / protein localization to centrosome ...cell differentiation involved in embryonic placenta development / regulation of cell differentiation involved in embryonic placenta development / primitive hemopoiesis / neural tube formation / positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / endocardium development / negative regulation of organ growth / hippo signaling / 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 / phosphatidylinositol 3-kinase/protein kinase B signal transduction / epithelial cell proliferation / central nervous system development / protein tetramerization / positive regulation of JNK cascade / negative regulation of canonical Wnt signaling pathway / positive regulation of DNA-binding transcription factor activity / protein import into nucleus / negative regulation of epithelial cell proliferation / positive regulation of protein binding / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein stabilization / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / positive regulation of apoptotic process / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / apoptotic process / magnesium ion binding / protein-containing complex / ATP binding / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
: / Mst1 SARAH domain / C terminal SARAH domain of Mst1 / SARAH domain / SARAH domain profile. / p53-like tetramerisation domain superfamily / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. ...: / Mst1 SARAH domain / C terminal SARAH domain of Mst1 / SARAH domain / SARAH domain profile. / p53-like tetramerisation domain superfamily / 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
Chem-5BS / Serine/threonine-protein kinase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.901 Å
AuthorsNawrotek, A. / Vuillard, L. / Miallau, L. / Weber, C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of the Kelch domain of human Keap1in complex with ligand S217879
Authors: Weber, C. / Vuillard, L. / Delerive, P. / Miallau, L. / Nawrotek, A.
History
DepositionJun 16, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 20, 2022Provider: repository / Type: Initial release
Revision 2.0Dec 7, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / cell ...atom_site / cell / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_mod_residue / pdbx_unobs_or_zero_occ_residues / pdbx_validate_torsion / struct_asym / struct_conf / struct_conn / struct_ref / struct_ref_seq
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.occupancy / _atom_site.pdbx_formal_charge / _atom_site.type_symbol / _cell.Z_PDB / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.entity_id / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_validate_torsion.auth_seq_id / _struct_conf.beg_auth_comp_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_comp_id / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_class / _struct_conf.pdbx_PDB_helix_length / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.ref_id
Revision 2.1May 1, 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: Serine/threonine-protein kinase 3 36kDa subunit
B: Serine/threonine-protein kinase 3 36kDa subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,8876
Polymers68,0082
Non-polymers8794
Water3,873215
1
A: Serine/threonine-protein kinase 3 36kDa subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3864
Polymers33,9241
Non-polymers4623
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Serine/threonine-protein kinase 3 36kDa subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5002
Polymers34,0841
Non-polymers4161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.77, 99.04, 167.29
Angle α, β, γ (deg.)90, 90, 90
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Serine/threonine-protein kinase 3 36kDa subunit / MST2/N


Mass: 33923.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STK3, KRS1, MST2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13188
#2: Protein Serine/threonine-protein kinase 3 36kDa subunit / MST2/N


Mass: 34083.828 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STK3, KRS1, MST2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13188
#3: Chemical ChemComp-5BS / 4-[(5,10-dimethyl-6-oxo-6,10-dihydro-5H-pyrimido[5,4-b]thieno[3,2-e][1,4]diazepin-2-yl)amino]benzenesulfonamide


Mass: 416.477 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H16N6O3S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: 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: 2.74 Å3/Da / Density % sol: 55.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M Ammonium citrate pH 7.0 and 18% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98012 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jan 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98012 Å / Relative weight: 1
ReflectionResolution: 1.852→83.644 Å / Num. obs: 32603 / % possible obs: 92.6 % / Redundancy: 13.3 % / CC1/2: 0.998 / CC star: 0.605 / Net I/σ(I): 14.8
Reflection shellResolution: 1.852→2.104 Å / Rmerge(I) obs: 1.402 / Num. unique obs: 1630 / CC1/2: 0.605

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Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
autoPROCdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: in-house

Resolution: 1.901→66.92 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.905 / SU R Cruickshank DPI: 0.288 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.292 / SU Rfree Blow DPI: 0.222 / SU Rfree Cruickshank DPI: 0.223
RfactorNum. reflection% reflectionSelection details
Rfree0.2575 1698 -RANDOM
Rwork0.2182 ---
obs0.2202 33405 56.1 %-
Displacement parametersBiso mean: 39.99 Å2
Baniso -1Baniso -2Baniso -3
1--1.0103 Å20 Å20 Å2
2---0.3871 Å20 Å2
3---1.3974 Å2
Refine analyzeLuzzati coordinate error obs: 0.31 Å
Refinement stepCycle: LAST / Resolution: 1.901→66.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4417 0 80 215 4712
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0084649HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.046320HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1643SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes820HARMONIC5
X-RAY DIFFRACTIONt_it4649HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion630SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact3895SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.89
X-RAY DIFFRACTIONt_other_torsion19.5
LS refinement shellResolution: 1.901→2 Å
RfactorNum. reflection% reflection
Rfree0.4053 24 -
Rwork0.2928 --
obs--7.93 %

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