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- PDB-8ycm: Monomeric Human STK19 -

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Basic information

Entry
Database: PDB / ID: 8ycm
TitleMonomeric Human STK19
ComponentsIsoform 4 of Inactive serine/threonine-protein kinase 19
KeywordsDNA BINDING PROTEIN / Winged helix domain protein / DNA binding / RNA binding / DNA repair
Function / homology
Function and homology information


positive regulation of single strand break repair / positive regulation of Ras protein signal transduction / kinase activity / double-stranded RNA binding / double-stranded DNA binding / nuclear speck / protein homodimerization activity / ATP binding / nucleus / cytoplasm
Similarity search - Function
Serine-threonine protein kinase 19 / Inactive serine-threonine protein kinase 19
Similarity search - Domain/homology
Winged helix repair factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.32 Å
AuthorsLi, J. / Ma, X. / Dong, Z.
Funding support China, 1items
OrganizationGrant numberCountry
Other governmentNo. 221100310100 China
CitationJournal: Sci Rep / Year: 2024
Title: Mutations found in cancer patients compromise DNA binding of the winged helix protein STK19.
Authors: Li, J. / Ma, X. / Wang, X. / Hu, X. / Fang, S. / Jin, G. / Liu, K. / Dong, Z.
History
DepositionFeb 18, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jul 3, 2024Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Isoform 4 of Inactive serine/threonine-protein kinase 19
B: Isoform 4 of Inactive serine/threonine-protein kinase 19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7005
Polymers50,4122
Non-polymers2883
Water6,467359
1
A: Isoform 4 of Inactive serine/threonine-protein kinase 19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3983
Polymers25,2061
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Isoform 4 of Inactive serine/threonine-protein kinase 19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3022
Polymers25,2061
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.322, 97.836, 98.657
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Isoform 4 of Inactive serine/threonine-protein kinase 19 / Protein G11 / Protein RP1


Mass: 25205.914 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STK19, G11, RP1 / Production host: Escherichia coli (E. coli) / References: UniProt: P49842
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 359 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.7 Å3/Da / Density % sol: 54.4 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Bis-Tris pH 6.3, 2 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17B1 / Wavelength: 0.977 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 9, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 1.32→49.33 Å / Num. obs: 125371 / % possible obs: 99.8 % / Redundancy: 6.5 % / Biso Wilson estimate: 14.49 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.06 / Net I/σ(I): 17.1
Reflection shellResolution: 1.32→1.34 Å / Rmerge(I) obs: 1.368 / Num. unique obs: 5979 / CC1/2: 0.553

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.32→31.17 Å / SU ML: 0.1499 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.8206
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1955 1995 1.59 %
Rwork0.1762 123254 -
obs0.1765 125249 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.53 Å2
Refinement stepCycle: LAST / Resolution: 1.32→31.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3491 0 15 359 3865
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00993685
X-RAY DIFFRACTIONf_angle_d1.26095016
X-RAY DIFFRACTIONf_chiral_restr0.081573
X-RAY DIFFRACTIONf_plane_restr0.0087653
X-RAY DIFFRACTIONf_dihedral_angle_d19.15721373
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.32-1.360.30761450.27628533X-RAY DIFFRACTION98.19
1.36-1.390.27311370.24858711X-RAY DIFFRACTION99.94
1.39-1.430.25181430.22828760X-RAY DIFFRACTION99.92
1.43-1.480.22961380.21168735X-RAY DIFFRACTION99.93
1.48-1.530.23251420.19158729X-RAY DIFFRACTION99.83
1.53-1.590.22341430.18068761X-RAY DIFFRACTION99.89
1.59-1.670.2341450.17128756X-RAY DIFFRACTION99.98
1.67-1.750.19271410.16498770X-RAY DIFFRACTION99.98
1.75-1.860.17451430.16028782X-RAY DIFFRACTION99.94
1.86-2.010.16511420.15348829X-RAY DIFFRACTION99.88
2.01-2.210.15921460.14558838X-RAY DIFFRACTION99.76
2.21-2.530.15941420.15588877X-RAY DIFFRACTION99.94
2.53-3.180.19851420.17958950X-RAY DIFFRACTION99.87
3.19-31.170.20211460.18359223X-RAY DIFFRACTION99.54

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