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- PDB-9flq: Crystal structure of human Haspin (GSG2) kinase bound to MU1959 -

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Basic information

Entry
Database: PDB / ID: 9flq
TitleCrystal structure of human Haspin (GSG2) kinase bound to MU1959
ComponentsSerine/threonine-protein kinase haspin
KeywordsTRANSFERASE / Haspin / Kinase / Inhibitor
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 / protein phosphorylation / non-specific serine/threonine protein kinase / protein kinase activity ...histone H3T3 kinase activity / protein localization to chromosome, centromeric region / mitotic sister chromatid cohesion / mitotic spindle assembly checkpoint signaling / spindle / mitotic cell cycle / chromosome / protein phosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / 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
: / NICKEL (II) ION / Serine/threonine-protein kinase haspin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsKraemer, A. / Paruch, K. / Knapp, S. / Structural Genomics Consortium (SGC)
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Innovative Medicines Initiative875510 Switzerland
CitationJournal: To Be Published
Title: Crystal structure of human Haspin (GSG2) kinase bound to MU1959
Authors: Kraemer, A. / Paruch, K. / Knapp, S. / Structural Genomics Consortium (SGC)
History
DepositionJun 5, 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)41,95111
Polymers40,7111
Non-polymers1,23910
Water3,837213
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2910 Å2
ΔGint-72 kcal/mol
Surface area15130 Å2
Unit cell
Length a, b, c (Å)68.590, 77.993, 87.098
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 6 types, 223 molecules

#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-A1IDD / [4-[5-(1-methylpyrazol-4-yl)pyrazolo[1,5-a]pyrimidin-3-yl]pyridin-2-yl]methanamine


Mass: 305.337 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H15N7 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.86 Å3/Da / Density % sol: 57.01 %
Crystal growTemperature: 278 K / Method: vapor diffusion / Details: 60% MPD, 0.1M MMT pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99999 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 3, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 1.85→44.37 Å / Num. obs: 40168 / % possible obs: 98.9 % / Redundancy: 13.4 % / CC1/2: 0.999 / Net I/σ(I): 14.2
Reflection shellResolution: 1.85→1.89 Å / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2261 / CC1/2: 0.762

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→44.37 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.963 / SU B: 2.915 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20198 1933 4.8 %RANDOM
Rwork0.17496 ---
obs0.17625 38175 98.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.859 Å2
Baniso -1Baniso -2Baniso -3
1-2.74 Å20 Å2-0 Å2
2---0.18 Å20 Å2
3----2.56 Å2
Refinement stepCycle: 1 / Resolution: 1.85→44.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2619 0 81 213 2913
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0122787
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162663
X-RAY DIFFRACTIONr_angle_refined_deg1.3361.6573777
X-RAY DIFFRACTIONr_angle_other_deg0.4491.5896142
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4865335
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.378512
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.8210491
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0640.2423
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023289
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02619
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_it2.1453.0441332
X-RAY DIFFRACTIONr_mcbond_other2.1443.0451333
X-RAY DIFFRACTIONr_mcangle_it3.0035.4531669
X-RAY DIFFRACTIONr_mcangle_other3.0035.4531670
X-RAY DIFFRACTIONr_scbond_it3.5363.5971455
X-RAY DIFFRACTIONr_scbond_other3.5353.5991456
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.5146.4012109
X-RAY DIFFRACTIONr_long_range_B_refined7.1332.353124
X-RAY DIFFRACTIONr_long_range_B_other7.12932.363125
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 125 -
Rwork0.324 2623 -
obs--93.5 %

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