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- PDB-3e7v: Crystal Structure of Human Haspin with a pyrazolo-pyrimidine ligand -

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Basic information

Entry
Database: PDB / ID: 3e7v
TitleCrystal Structure of Human Haspin with a pyrazolo-pyrimidine ligand
ComponentsSerine/threonine-protein kinase haspin
KeywordsTRANSFERASE / Haspin / Germ cell associated 2 (haspin) / Haploid germ cell specific nuclear protein kinase / SGC / structural genomics consortium / ATP-binding / Cell cycle / Chromatin regulator / Kinase / Magnesium / Nucleotide-binding / Nucleus / Phosphoprotein / Serine/threonine-protein kinase
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-DZO / NICKEL (II) ION / Serine/threonine-protein kinase haspin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsFilippakopoulos, P. / Eswaran, J. / Keates, T. / Burgess-Brown, N. / Fedorov, O. / Pike, A.C.W. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Wickstroem, M. ...Filippakopoulos, P. / Eswaran, J. / Keates, T. / Burgess-Brown, N. / Fedorov, O. / Pike, A.C.W. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Wickstroem, M. / Bountra, C. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal Structure of Human Haspin with a pyrazolo-pyrimidine ligand
Authors: Filippakopoulos, P. / Eswaran, J. / Keates, T. / Burgess-Brown, N. / Fedorov, O. / Pike, A.C.W. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Wickstroem, M. / Bountra, C. / Knapp, S.
History
DepositionAug 19, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jan 31, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.3Aug 30, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _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)41,54010
Polymers40,7111
Non-polymers8299
Water5,423301
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.497, 86.952, 68.460
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 / Haploid germ cell-specific nuclear protein kinase / H-haspin / Germ cell-specific gene 2 protein


Mass: 40711.484 Da / Num. of mol.: 1 / Fragment: UNP residues 471-798
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GSG2 / 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-DZO / 3-(3-aminophenyl)-N-(3-chlorophenyl)pyrazolo[1,5-a]pyrimidin-5-amine


Mass: 335.790 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H14ClN5
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 301 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.87 Å3/Da / Density % sol: 57.13 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M PCB, 30% PEG 1K , pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 26, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5 Å / Relative weight: 1
ReflectionResolution: 2→25.44 Å / Num. obs: 32235 / % possible obs: 99.8 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.079 / Rsym value: 0.079 / Net I/σ(I): 10.2
Reflection shellResolution: 2→2.11 Å / Redundancy: 3 % / Rmerge(I) obs: 0.503 / Mean I/σ(I) obs: 2.1 / Num. unique all: 4630 / Rsym value: 0.503 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.4.0066refinement
CrystalCleardata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2VUW

2vuw


Resolution: 2→25.44 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.935 / SU B: 6.553 / SU ML: 0.097 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.136 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22462 1428 4.4 %RANDOM
Rwork0.16771 ---
all0.17017 ---
obs0.17017 30770 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.008 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å20 Å20 Å2
2---1.07 Å20 Å2
3---1.34 Å2
Refinement stepCycle: LAST / Resolution: 2→25.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2602 0 53 301 2956
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222734
X-RAY DIFFRACTIONr_bond_other_d0.0010.021870
X-RAY DIFFRACTIONr_angle_refined_deg1.4531.9713684
X-RAY DIFFRACTIONr_angle_other_deg1.6323.0014555
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.915327
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.02324.309123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.5415484
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7481513
X-RAY DIFFRACTIONr_chiral_restr0.0840.2407
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022980
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02540
X-RAY DIFFRACTIONr_mcbond_it3.31731634
X-RAY DIFFRACTIONr_mcbond_other1.123663
X-RAY DIFFRACTIONr_mcangle_it4.44152652
X-RAY DIFFRACTIONr_scbond_it6.98481100
X-RAY DIFFRACTIONr_scangle_it9.286111032
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 105 -
Rwork0.238 2241 -
obs--100 %
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)
11.0677-0.29510.37110.1676-0.09640.4447-0.0284-0.0393-0.01360.00890.0315-0.0142-0.0168-0.0044-0.00310.0206-0.0112-0.0038-0.00770.0010.056213.363-18.685-3.911
20.6960.0927-0.37350.8443-0.230.72250.05760.00080.1469-0.0265-0.0372-0.0614-0.06210.0004-0.02040.0082-0.00370.0032-0.01590.02250.06310.891-0.604-13.803
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA471 - 60930 - 168
2X-RAY DIFFRACTION2AA610 - 798169 - 357

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