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- PDB-6g37: Crystal structure of haspin in complex with 5-fluorotubercidin -

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Basic information

Entry
Database: PDB / ID: 6g37
TitleCrystal structure of haspin in complex with 5-fluorotubercidin
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 / 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 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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
5-fluorotubercidin / PHOSPHATE ION / Serine/threonine-protein kinase haspin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 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)41,0913
Polymers40,7111
Non-polymers3792
Water3,873215
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area50 Å2
ΔGint-2 kcal/mol
Surface area14990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.711, 78.890, 79.630
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 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): R3
References: UniProt: Q8TF76, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-FTU / 5-fluorotubercidin


Mass: 284.244 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H13FN4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 3.04 Å3/Da / Density % sol: 59.49 %
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: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.48→23.8 Å / Num. obs: 83206 / % possible obs: 100 % / Redundancy: 9.3 % / CC1/2: 0.994 / Rmerge(I) obs: 0.149 / Net I/σ(I): 9.9
Reflection shellResolution: 1.48→1.51 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 2.5 / Num. unique obs: 4087 / CC1/2: 0.648 / % possible all: 100

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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: 1.48→23.8 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.764 / SU ML: 0.033 / Cross valid method: THROUGHOUT / ESU R: 0.051 / ESU R Free: 0.048 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16741 4122 5 %RANDOM
Rwork0.14823 ---
obs0.14916 79010 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 19.777 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å2-0 Å2-0 Å2
2---1.05 Å20 Å2
3---0.86 Å2
Refinement stepCycle: 1 / Resolution: 1.48→23.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2590 0 25 215 2830
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0192702
X-RAY DIFFRACTIONr_bond_other_d0.0020.022548
X-RAY DIFFRACTIONr_angle_refined_deg1.6051.9553667
X-RAY DIFFRACTIONr_angle_other_deg0.97835878
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3685336
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.39324.286119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.97515475
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8911512
X-RAY DIFFRACTIONr_chiral_restr0.1070.2414
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023081
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02625
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_it1.1220.9351317
X-RAY DIFFRACTIONr_mcbond_other1.1210.9361318
X-RAY DIFFRACTIONr_mcangle_it1.3481.4051649
X-RAY DIFFRACTIONr_mcangle_other1.3481.9211648
X-RAY DIFFRACTIONr_scbond_it1.6661.3811385
X-RAY DIFFRACTIONr_scbond_other1.6651.3811385
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.9472014
X-RAY DIFFRACTIONr_long_range_B_refined2.1633174
X-RAY DIFFRACTIONr_long_range_B_other2.1633175
X-RAY DIFFRACTIONr_rigid_bond_restr5.56732676
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded5.76552616
LS refinement shellResolution: 1.48→1.518 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 356 -
Rwork0.202 5725 -
obs--99.93 %
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)
12.10770.2171-0.81820.6474-0.04591.0915-0.00660.03160.1178-0.04330.0589-0.0957-0.05260.0621-0.05220.03830.00360.01270.0299-0.0050.026314.748915.87914.6692
21.99260.16840.45972.1119-0.31581.91630.0143-0.0009-0.11190.05010.015-0.06970.10260.0181-0.02930.00790.0014-0.00320.01090.00730.0141.58461.753114.3703
33.4235-0.30960.74672.7697-1.29814.64250.0848-0.5086-0.00460.4969-0.06540.0539-0.0074-0.1308-0.01950.1258-0.0440.0190.10540.03010.0617-5.5046-5.036426.4113
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A31 - 168
2X-RAY DIFFRACTION2A169 - 321
3X-RAY DIFFRACTION3A322 - 357

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