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- PDB-6g39: Crystal structure of haspin F605Y mutant in complex with 5-iodotu... -

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Basic information

Entry
Database: PDB / ID: 6g39
TitleCrystal structure of haspin F605Y mutant in complex with 5-iodotubercidin
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
Chem-5ID / IODIDE ION / Serine/threonine-protein kinase haspin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 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)41,5066
Polymers40,7271
Non-polymers7785
Water6,107339
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint-9 kcal/mol
Surface area15400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.820, 78.990, 79.540
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: 40727.484 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 , 5 types, 344 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-5ID / (2R,3R,4S,5R)-2-(4-AMINO-5-IODO-7H-PYRROLO[2,3-D]PYRIMIDIN-7-YL)-5-(HYDROXYMETHYL)TETRAHYDROFURAN-3,4-DIOL / 5-IODOTUBERCIDIN


Mass: 392.150 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H13IN4O4
#4: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: I
#5: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 339 / 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: 59.54 %
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: 1.45→22.01 Å / Num. obs: 86860 / % possible obs: 98.3 % / Redundancy: 5.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.2
Reflection shellResolution: 1.45→1.53 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 3 / Num. unique obs: 12366 / CC1/2: 0.801 / % possible all: 96.9

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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: 1.45→22.01 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.838 / SU ML: 0.035 / Cross valid method: THROUGHOUT / ESU R: 0.049 / ESU R Free: 0.051 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17543 4376 5 %RANDOM
Rwork0.15762 ---
obs0.15856 82433 98.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 25.173 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å20 Å2-0 Å2
2---0.68 Å20 Å2
3---0.27 Å2
Refinement stepCycle: 1 / Resolution: 1.45→22.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2628 0 38 339 3005
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0192861
X-RAY DIFFRACTIONr_bond_other_d0.0020.022747
X-RAY DIFFRACTIONr_angle_refined_deg1.6441.9633898
X-RAY DIFFRACTIONr_angle_other_deg0.9436361
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4945362
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.18124.219128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.20915522
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4761514
X-RAY DIFFRACTIONr_chiral_restr0.1050.2439
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023310
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02664
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_it0.9081.4011352
X-RAY DIFFRACTIONr_mcbond_other0.8981.3991351
X-RAY DIFFRACTIONr_mcangle_it1.4232.1011698
X-RAY DIFFRACTIONr_mcangle_other1.4262.1031699
X-RAY DIFFRACTIONr_scbond_it1.661.6471509
X-RAY DIFFRACTIONr_scbond_other1.6591.6491510
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.6452.3892185
X-RAY DIFFRACTIONr_long_range_B_refined6.47813.9813482
X-RAY DIFFRACTIONr_long_range_B_other6.47713.9933483
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded15.66553
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 267 -
Rwork0.238 6006 -
obs--96.42 %
Refinement TLS params.Method: refined / Origin x: 72.6622 Å / Origin y: 32.7252 Å / Origin z: 11.8296 Å
111213212223313233
T0.0155 Å20.0117 Å20.0047 Å2-0.012 Å20.0006 Å2--0.0102 Å2
L1.7604 °20.6234 °20.445 °2-1.1298 °20.3252 °2--0.9728 °2
S0.028 Å °-0.0439 Å °0.07 Å °0.0233 Å °0.0131 Å °0.0653 Å °-0.0496 Å °-0.0381 Å °-0.0412 Å °

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