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- PDB-9flc: Crystal structure of haspin (GSG2) in complex with MU1668 -

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Basic information

Entry
Database: PDB / ID: 9flc
TitleCrystal structure of haspin (GSG2) in complex with MU1668
ComponentsSerine/threonine-protein kinase haspin
KeywordsTRANSFERASE / kinase / haspin / inhibitor / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


histone H3T3 kinase activity / protein localization to chromosome, centromeric region / mitotic sister chromatid cohesion / mitotic spindle assembly checkpoint signaling / spindle / mitotic cell cycle / chromosome / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction ...histone H3T3 kinase activity / protein localization to chromosome, centromeric region / mitotic sister chromatid cohesion / mitotic spindle assembly checkpoint signaling / spindle / mitotic cell cycle / chromosome / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / protein phosphorylation / protein serine kinase activity / centrosome / nucleoplasm / ATP binding / nucleus / cytoplasm
Similarity search - Function
Serine/threonine-protein kinase haspin, C-terminal / Haspin like kinase domain / Domain of unknown function / 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 haspin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å
AuthorsChaikuad, A. / Paruch, K. / Knapp, S. / Structural Genomics Consortium (SGC)
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of haspin (GSG2) in complex with MU1668
Authors: Chaikuad, A. / Paruch, K. / Knapp, S. / Structural Genomics Consortium (SGC)
History
DepositionJun 4, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein kinase haspin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2144
Polymers40,7111
Non-polymers5033
Water3,117173
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint-7 kcal/mol
Surface area15440 Å2
Unit cell
Length a, b, c (Å)77.822, 77.908, 81.313
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 haspin / Germ cell-specific gene 2 protein / H-haspin / Haploid germ cell-specific nuclear protein kinase


Mass: 40711.484 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HASPIN, GSG2 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8TF76, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-A1IDA / 5-(1-methylpyrazol-3-yl)-3-pyridin-4-yl-thieno[3,2-b]pyridine


Mass: 292.358 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H12N4S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 173 / 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: 3.03 Å3/Da / Density % sol: 59.37 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 63% MPD, 0.1M SPG 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 18, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.18→45.59 Å / Num. obs: 26473 / % possible obs: 100 % / Redundancy: 7.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.062 / Rrim(I) all: 0.124 / Χ2: 0.99 / Net I/σ(I): 11.1
Reflection shellResolution: 2.18→2.26 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.973 / Mean I/σ(I) obs: 2 / Num. unique obs: 2545 / CC1/2: 0.724 / Rpim(I) all: 0.396 / Rrim(I) all: 1.051 / Χ2: 1.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.18→45.59 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.952 / SU B: 8.688 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.166 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19705 1294 4.9 %RANDOM
Rwork0.16485 ---
obs0.1663 25128 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.187 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å2-0 Å2-0 Å2
2---1.42 Å20 Å2
3---1.11 Å2
Refinement stepCycle: 1 / Resolution: 2.18→45.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2627 0 35 173 2835
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0132729
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172531
X-RAY DIFFRACTIONr_angle_refined_deg1.3821.6333688
X-RAY DIFFRACTIONr_angle_other_deg1.3281.5825892
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1125329
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.89523.185135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.77515492
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.8161512
X-RAY DIFFRACTIONr_chiral_restr0.0720.2351
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.023123
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02561
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_it2.1433.0761314
X-RAY DIFFRACTIONr_mcbond_other2.1423.0761314
X-RAY DIFFRACTIONr_mcangle_it3.1244.6051640
X-RAY DIFFRACTIONr_mcangle_other3.1234.6051641
X-RAY DIFFRACTIONr_scbond_it3.3663.4961415
X-RAY DIFFRACTIONr_scbond_other3.3653.4981416
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2745.0712048
X-RAY DIFFRACTIONr_long_range_B_refined6.71436.8913146
X-RAY DIFFRACTIONr_long_range_B_other6.71336.9083147
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.18→2.237 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 107 -
Rwork0.249 1829 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 5.9654 Å / Origin y: -6.2618 Å / Origin z: 28.8207 Å
111213212223313233
T0.0219 Å2-0.0087 Å20.0002 Å2-0.0066 Å20.0048 Å2--0.031 Å2
L0.8445 °2-0.5576 °20.1985 °2-0.744 °2-0.2644 °2--0.594 °2
S0.0038 Å °-0.0214 Å °0.0843 Å °-0.03 Å °0.0202 Å °-0.1035 Å °-0.0471 Å °-0.0131 Å °-0.024 Å °

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