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- PDB-6g36: Crystal structure of haspin in complex with 5-chlorotubercidin -

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Basic information

Entry
Database: PDB / ID: 6g36
TitleCrystal structure of haspin in complex with 5-chlorotubercidin
ComponentsSerine/threonine-protein kinase haspin
KeywordsTRANSFERASE / kinase / inhibitors / slow off-rate / kinetics / halogen / 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
: / 5-chlorotubercidin / PHOSPHATE ION / Serine/threonine-protein kinase haspin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 Å
AuthorsHeroven, C. / Chaikuad, A. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2018
Title: Halogen-Aromatic pi Interactions Modulate Inhibitor Residence Times.
Authors: Heroven, C. / Georgi, V. / Ganotra, G.K. / Brennan, P. / Wolfreys, F. / Wade, R.C. / Fernandez-Montalvan, A.E. / Chaikuad, A. / Knapp, S.
History
DepositionMar 24, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 18, 2018Provider: repository / Type: Initial release
Revision 1.1May 16, 2018Group: Data collection / Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.name
Revision 1.2Jun 13, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 17, 2024Group: 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 haspin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6148
Polymers40,7111
Non-polymers9037
Water4,558253
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-33 kcal/mol
Surface area15570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.740, 78.910, 79.820
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 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): R3
References: UniProt: Q8TF76, non-specific serine/threonine protein kinase

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Non-polymers , 7 types, 260 molecules

#2: Chemical ChemComp-EKH / 5-chlorotubercidin


Mass: 300.698 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H13ClN4O4
#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: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#6: 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
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / 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: 3.01 Å3/Da / Density % sol: 59.09 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 51-63% MPD and 0.1M SPG buffer, pH 6.0-6.5 / PH range: 6.0-6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 30, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.46→23.78 Å / Num. obs: 85664 / % possible obs: 99.8 % / Redundancy: 6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.075 / Net I/σ(I): 12.3
Reflection shellResolution: 1.46→1.48 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.629 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 4145 / CC1/2: 0.741 / % possible all: 98.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OUC

4ouc


Resolution: 1.46→23.78 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.781 / SU ML: 0.035 / Cross valid method: THROUGHOUT / ESU R: 0.052 / ESU R Free: 0.05 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17564 4170 4.9 %RANDOM
Rwork0.14945 ---
obs0.15069 81420 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 22.125 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å20 Å2-0 Å2
2---1 Å20 Å2
3---0.5 Å2
Refinement stepCycle: 1 / Resolution: 1.46→23.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2678 0 53 253 2984
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0192862
X-RAY DIFFRACTIONr_bond_other_d0.0020.022699
X-RAY DIFFRACTIONr_angle_refined_deg1.6081.9643882
X-RAY DIFFRACTIONr_angle_other_deg0.97736241
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5375355
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.4824.444126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.70715506
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9261512
X-RAY DIFFRACTIONr_chiral_restr0.1080.2431
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023271
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02663
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_it1.311.2521388
X-RAY DIFFRACTIONr_mcbond_other1.3121386
X-RAY DIFFRACTIONr_mcangle_it1.4861.881744
X-RAY DIFFRACTIONr_mcangle_other1.4851.8811745
X-RAY DIFFRACTIONr_scbond_it1.7522.6131474
X-RAY DIFFRACTIONr_scbond_other1.7512.6131474
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.0262136
X-RAY DIFFRACTIONr_long_range_B_refined2.2033377
X-RAY DIFFRACTIONr_long_range_B_other2.2023378
X-RAY DIFFRACTIONr_rigid_bond_restr5.36632812
X-RAY DIFFRACTIONr_sphericity_free11.41151
X-RAY DIFFRACTIONr_sphericity_bonded6.29352744
LS refinement shellResolution: 1.46→1.498 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.231 316 -
Rwork0.221 5893 -
obs--98.7 %
Refinement TLS params.Method: refined / Origin x: 6.0606 Å / Origin y: 7.2305 Å / Origin z: 11.4114 Å
111213212223313233
T0.008 Å20.005 Å2-0.0049 Å2-0.013 Å20.0001 Å2--0.0102 Å2
L1.7427 °20.8295 °2-0.5285 °2-1.1613 °2-0.4833 °2--0.9603 °2
S-0.002 Å °-0.0192 Å °-0.0783 Å °-0.0188 Å °0.0476 Å °-0.0378 Å °0.0609 Å °0.0001 Å °-0.0456 Å °

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