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- PDB-3com: Crystal structure of Mst1 kinase -

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Basic information

Entry
Database: PDB / ID: 3com
TitleCrystal structure of Mst1 kinase
ComponentsSerine/threonine-protein kinase 4Serine/threonine-specific protein kinase
KeywordsTRANSFERASE / kinase / Mst1 / Serine/threonine-protein kinase 4 / STE20-like kinase / PSI / structural genomics / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC / Alternative splicing / Apoptosis / ATP-binding / Coiled coil / Cytoplasm / Magnesium / Metal-binding / Nucleotide-binding / Nucleus / Phosphoprotein / Polymorphism
Function / homology
Function and homology information


positive regulation of hepatocyte apoptotic process / 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 / positive regulation of substrate-dependent cell migration, cell attachment to substrate / endocardium development / negative regulation of organ growth / hippo signaling ...positive regulation of hepatocyte apoptotic process / 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 / positive regulation of substrate-dependent cell migration, cell attachment to substrate / endocardium development / negative regulation of organ growth / hippo signaling / Signaling by Hippo / organ growth / branching involved in blood vessel morphogenesis / hepatocyte apoptotic process / regulation of MAPK cascade / extrinsic apoptotic signaling pathway via death domain receptors / canonical Wnt signaling pathway / positive regulation of fat cell differentiation / keratinocyte differentiation / protein serine/threonine kinase activator activity / epithelial cell proliferation / central nervous system development / protein tetramerization / negative regulation of canonical Wnt signaling pathway / cell morphogenesis / protein import into nucleus / negative regulation of epithelial cell proliferation / positive regulation of peptidyl-serine phosphorylation / positive regulation of protein binding / peptidyl-serine phosphorylation / RNA polymerase II-specific DNA-binding transcription factor binding / protein autophosphorylation / protein stabilization / nuclear body / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / positive regulation of protein phosphorylation / positive regulation of apoptotic process / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / magnesium ion binding / signal transduction / protein homodimerization activity / protein-containing complex / nucleoplasm / 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-like tetramerisation domain superfamily / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase domain ...Mst1 SARAH domain / C terminal SARAH domain of Mst1 / SARAH domain / SARAH domain profile. / p53-like tetramerisation domain superfamily / 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
Serine/threonine-protein kinase 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsAtwell, S. / Burley, S.K. / Dickey, M. / Leon, B. / Sauder, J.M. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of Mst1 kinase.
Authors: Atwell, S. / Burley, S.K. / Dickey, M. / Leon, B. / Sauder, J.M.
History
DepositionMar 28, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.5Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein kinase 4
B: Serine/threonine-protein kinase 4


Theoretical massNumber of molelcules
Total (without water)71,5882
Polymers71,5882
Non-polymers00
Water4,161231
1
A: Serine/threonine-protein kinase 4


Theoretical massNumber of molelcules
Total (without water)35,7941
Polymers35,7941
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Serine/threonine-protein kinase 4


Theoretical massNumber of molelcules
Total (without water)35,7941
Polymers35,7941
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.977, 105.151, 110.955
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 4 / Serine/threonine-specific protein kinase / STE20-like kinase MST1 / MST-1 / Mammalian STE20-like protein kinase 1 / Serine/threonine-protein kinase Krs-2


Mass: 35793.863 Da / Num. of mol.: 2 / Fragment: Protein kinase domain: Residues 2-311
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STK4, MST1 / Plasmid: pSGX4 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q13043, non-specific serine/threonine protein kinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 231 / 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: 3.05 Å3/Da / Density % sol: 59.74 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 10.5
Details: 1700mM Ammonium sulfate, 300mM Lithium sulfate, 100mM CAPS pH 10.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9794 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 1, 2004 / Details: KV mirrors
RadiationMonochromator: Kohzu 111 diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 40513 / % possible obs: 90.2 % / Redundancy: 3.2 % / Biso Wilson estimate: 27.2 Å2 / Rmerge(I) obs: 0.118 / Net I/σ(I): 6.5
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.439 / Mean I/σ(I) obs: 2.7 / Num. unique all: 6082 / % possible all: 93.9

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Processing

Software
NameVersionClassification
MAR345data collection
MOLREPphasing
REFMAC5refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3CKW

3ckw


Resolution: 2.2→30 Å / Isotropic thermal model: Isotropic / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.244 2022 -random
Rwork0.208 ---
obs0.208 40443 90.2 %-
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4283 0 0 231 4514
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.015
X-RAY DIFFRACTIONr_bond_d_na
X-RAY DIFFRACTIONr_bond_d_prot
X-RAY DIFFRACTIONr_angle_refined_deg1.394
X-RAY DIFFRACTIONr_angle_d_na
X-RAY DIFFRACTIONr_angle_d_prot
X-RAY DIFFRACTIONr_angle_deg
X-RAY DIFFRACTIONr_angle_deg_na
X-RAY DIFFRACTIONr_angle_deg_prot
X-RAY DIFFRACTIONr_dihedral_angle_d
X-RAY DIFFRACTIONr_dihedral_angle_d_na
X-RAY DIFFRACTIONr_dihedral_angle_d_prot
X-RAY DIFFRACTIONr_improper_angle_d
X-RAY DIFFRACTIONr_improper_angle_d_na
X-RAY DIFFRACTIONr_improper_angle_d_prot
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it

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