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- PDB-5wi2: Crystal structure of the KA1 domain from human Chk1 -

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Basic information

Entry
Database: PDB / ID: 5wi2
TitleCrystal structure of the KA1 domain from human Chk1
ComponentscDNA FLJ56409, highly similar to Serine/threonine-protein kinase Chk1 (EC 2.7.11.1)
KeywordsTRANSFERASE / Kinase / Checkpoint / Autoinhibition
Function / homology
Function and homology information


negative regulation of G0 to G1 transition / apoptotic process involved in development / histone H3T11 kinase activity / negative regulation of DNA biosynthetic process / mitotic G2/M transition checkpoint / negative regulation of mitotic nuclear division / regulation of mitotic centrosome separation / inner cell mass cell proliferation / negative regulation of gene expression, epigenetic / regulation of double-strand break repair via homologous recombination ...negative regulation of G0 to G1 transition / apoptotic process involved in development / histone H3T11 kinase activity / negative regulation of DNA biosynthetic process / mitotic G2/M transition checkpoint / negative regulation of mitotic nuclear division / regulation of mitotic centrosome separation / inner cell mass cell proliferation / negative regulation of gene expression, epigenetic / regulation of double-strand break repair via homologous recombination / nucleus organization / cellular response to caffeine / Transcriptional Regulation by E2F6 / mitotic G2 DNA damage checkpoint signaling / Presynaptic phase of homologous DNA pairing and strand exchange / replicative senescence / signal transduction in response to DNA damage / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / Activation of ATR in response to replication stress / positive regulation of cell cycle / condensed nuclear chromosome / regulation of signal transduction by p53 class mediator / replication fork / DNA damage checkpoint signaling / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / TP53 Regulates Transcription of DNA Repair Genes / peptidyl-threonine phosphorylation / G2/M DNA damage checkpoint / Signaling by SCF-KIT / cellular response to mechanical stimulus / G2/M transition of mitotic cell cycle / regulation of cell population proliferation / Processing of DNA double-strand break ends / DNA replication / Regulation of TP53 Activity through Phosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / chromatin remodeling / protein domain specific binding / protein phosphorylation / intracellular membrane-bounded organelle / DNA repair / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / apoptotic process / DNA damage response / chromatin / protein-containing complex / extracellular space / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Checkpoint kinase 1, catalytic domain / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / 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
ACETATE ION / cDNA FLJ56409, highly similar to Serine/threonine-protein kinase Chk1 / Serine/threonine-protein kinase Chk1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.495 Å
AuthorsEmptage, R.P. / Marmorstein, R.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F32-GM115098 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P01-CA114046 United States
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Intramolecular autoinhibition of checkpoint kinase 1 is mediated by conserved basic motifs of the C-terminal kinase-associated 1 domain.
Authors: Emptage, R.P. / Schoenberger, M.J. / Ferguson, K.M. / Marmorstein, R.
History
DepositionJul 18, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 4, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Feb 7, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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

Downloads & links

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Assembly

Deposited unit
A: cDNA FLJ56409, highly similar to Serine/threonine-protein kinase Chk1 (EC 2.7.11.1)
B: cDNA FLJ56409, highly similar to Serine/threonine-protein kinase Chk1 (EC 2.7.11.1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3369
Polymers23,8902
Non-polymers4467
Water54030
1
A: cDNA FLJ56409, highly similar to Serine/threonine-protein kinase Chk1 (EC 2.7.11.1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1554
Polymers11,9451
Non-polymers2103
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: cDNA FLJ56409, highly similar to Serine/threonine-protein kinase Chk1 (EC 2.7.11.1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1815
Polymers11,9451
Non-polymers2364
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: cDNA FLJ56409, highly similar to Serine/threonine-protein kinase Chk1 (EC 2.7.11.1)
hetero molecules

A: cDNA FLJ56409, highly similar to Serine/threonine-protein kinase Chk1 (EC 2.7.11.1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3369
Polymers23,8902
Non-polymers4467
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_225-y-3,x-y-3,z1
Buried area1980 Å2
ΔGint-11 kcal/mol
Surface area10280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.818, 76.818, 31.828
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3

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Components

#1: Protein cDNA FLJ56409, highly similar to Serine/threonine-protein kinase Chk1 (EC 2.7.11.1)


Mass: 11945.033 Da / Num. of mol.: 2 / Fragment: KA1 domain residues 393-492
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: B4DT73, UniProt: O14757*PLUS
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.27 Å3/Da / Density % sol: 45.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.8 / Details: Sodium Acetate Trihydrate, Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.495→50 Å / Num. obs: 7313 / % possible obs: 99.9 % / Redundancy: 5 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 24.5

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2EHB

2ehb


Resolution: 2.495→38.409 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 2.08 / Phase error: 28.72
RfactorNum. reflection% reflection
Rfree0.2445 729 9.98 %
Rwork0.2136 --
obs0.2166 7308 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.495→38.409 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1435 0 30 30 1495
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061501
X-RAY DIFFRACTIONf_angle_d0.7372017
X-RAY DIFFRACTIONf_dihedral_angle_d16.178543
X-RAY DIFFRACTIONf_chiral_restr0.051236
X-RAY DIFFRACTIONf_plane_restr0.003251
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4949-2.68750.32021520.26331314X-RAY DIFFRACTION99
2.6875-2.95790.36231430.28141326X-RAY DIFFRACTION100
2.9579-3.38570.30941400.24911288X-RAY DIFFRACTION100
3.3857-4.26470.23711430.19941327X-RAY DIFFRACTION100
4.2647-38.41350.19331510.18851324X-RAY DIFFRACTION100

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