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- PDB-3f2n: Crystal Structure of Human Haspin with an Imidazo-pyridazine ligand -

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Basic information

Entry
Database: PDB / ID: 3f2n
TitleCrystal Structure of Human Haspin with an Imidazo-pyridazine ligand
ComponentsSerine/threonine-protein kinase haspin
KeywordsTRANSFERASE / Haspin / Germ cell associated 2 / haploid germ cell specific nuclear protein kinase / ATP-binding / Cell cycle / Chromatin regulator / Kinase / Magnesium / Nucleotide-binding / Nucleus / Phosphoprotein / Serine/threonine-protein kinase / 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 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. ...Serine/threonine-protein kinase haspin, C-terminal / Haspin like kinase domain / Domain of unknown function / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-IZZ / PHOSPHATE ION / Serine/threonine-protein kinase haspin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsFilippakopoulos, P. / Eswaran, J. / Keates, T. / Burgess-Brown, N. / Fedorov, O. / Yue, W.W. / Murray, J.W. / Pike, A.C.W. / Von Delft, F. / Arrowsmith, C.H. ...Filippakopoulos, P. / Eswaran, J. / Keates, T. / Burgess-Brown, N. / Fedorov, O. / Yue, W.W. / Murray, J.W. / Pike, A.C.W. / Von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bountra, C. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal Structure of Human Haspin with an Imidazo-pyridazine ligand
Authors: Filippakopoulos, P. / Eswaran, J. / Keates, T. / Burgess-Brown, N. / Fedorov, O. / Yue, W.W. / Murray, J.W. / Pike, A.C.W. / Von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / ...Authors: Filippakopoulos, P. / Eswaran, J. / Keates, T. / Burgess-Brown, N. / Fedorov, O. / Yue, W.W. / Murray, J.W. / Pike, A.C.W. / Von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bountra, C. / Knapp, S.
History
DepositionOct 30, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)41,4288
Polymers40,7111
Non-polymers7177
Water5,819323
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.416, 77.307, 85.575
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 / GSG2 / Haploid germ cell-specific nuclear protein kinase / H-haspin / Germ cell-specific gene 2 protein


Mass: 40711.484 Da / Num. of mol.: 1 / Fragment: Protein kinase, residues 471-798
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HASPIN / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3
References: UniProt: Q8TF76, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-IZZ / (2S)-2-{[3-(3-aminophenyl)imidazo[1,2-b]pyridazin-6-yl]amino}-3-methylbutan-1-ol


Mass: 311.382 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N5O
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 323 / 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: 2.94 Å3/Da / Density % sol: 58.19 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M Na/KPO4, 20% PEG 3350, 10% EtGly, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9789 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 26, 2008
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 1.8→57.35 Å / Num. all: 44667 / Num. obs: 44444 / % possible obs: 99.5 % / Redundancy: 3.5 % / Biso Wilson estimate: 23.6 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 11.8
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.462 / Mean I/σ(I) obs: 2 / Num. unique all: 6256 / Rsym value: 0.462 / % possible all: 96.9

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.5.0055refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VUW

2vuw


Resolution: 1.8→57.35 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.959 / SU B: 4.337 / SU ML: 0.061 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.093 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18553 1966 4.4 %RANDOM
Rwork0.16126 ---
all0.16235 42870 --
obs0.16235 42643 99.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.449 Å2
Baniso -1Baniso -2Baniso -3
1-0.69 Å20 Å20 Å2
2---0.08 Å20 Å2
3----0.61 Å2
Refinement stepCycle: LAST / Resolution: 1.8→57.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2613 0 48 323 2984
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222770
X-RAY DIFFRACTIONr_bond_other_d0.0010.021884
X-RAY DIFFRACTIONr_angle_refined_deg1.4381.9713740
X-RAY DIFFRACTIONr_angle_other_deg0.95234620
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1145329
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.57824.4125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.9115501
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.8881513
X-RAY DIFFRACTIONr_chiral_restr0.0920.2421
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022991
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02541
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_it2.79731648
X-RAY DIFFRACTIONr_mcbond_other0.9713665
X-RAY DIFFRACTIONr_mcangle_it4.05552688
X-RAY DIFFRACTIONr_scbond_it6.2271122
X-RAY DIFFRACTIONr_scangle_it8.748111052
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.805→1.852 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 132 -
Rwork0.275 2970 -
obs--94.98 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.74180.4981-0.15931.2618-0.5630.3508-0.0273-0.02440.00070.0031-0.0223-0.0646-0.05390.0420.04950.146-0.01480.0030.0808-0.01490.0447-3.89613.089-18.022
21.6901-0.4612-0.39510.83820.01841.20780.0251-0.21990.02350.10720.0667-0.023-0.1078-0.0551-0.09180.1210.01430.03640.09180.00070.0266-15.0780.435-0.369
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A471 - 610
2X-RAY DIFFRACTION2A611 - 798

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