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- PDB-2vuw: Structure of human haspin kinase domain -

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Basic information

Entry
Database: PDB / ID: 2vuw
TitleStructure of human haspin kinase domain
ComponentsSERINE/THREONINE-PROTEIN KINASE HASPIN
KeywordsTRANSFERASE / CELL CYCLE / CASP8 / NUCLEOTIDE BINDING
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 / intracellular signal transduction / 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 / non-specific serine/threonine protein kinase / intracellular signal transduction / protein kinase activity / 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-5ID / IODIDE ION / NICKEL (II) ION / Serine/threonine-protein kinase haspin
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsEswaran, J. / Murray, J.W. / Filippakopoulos, P. / Soundararajan, M. / Pike, A.C.W. / von Delft, F. / Picaud, S. / Keates, T. / King, O. / Wickstroem, M. ...Eswaran, J. / Murray, J.W. / Filippakopoulos, P. / Soundararajan, M. / Pike, A.C.W. / von Delft, F. / Picaud, S. / Keates, T. / King, O. / Wickstroem, M. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Fedorov, O. / Burgess-Brown, N. / Bray, J. / Knapp, S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Structure and Functional Characterization of the Atypical Human Kinase Haspin.
Authors: Eswaran, J. / Patnaik, D. / Filippakopoulos, P. / Wang, F. / Stein, R.L. / Murray, J.W. / Higgins, J.M.G. / Knapp, S.
History
DepositionMay 30, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 16, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 2.0May 1, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)39,3896
Polymers38,6151
Non-polymers7745
Water7,170398
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)78.661, 78.775, 79.860
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 / HASPIN / HAPLOID GERM CELL-SPECIFIC NUCLEAR PROTEIN KINASE / H-HASPIN / GERM CELL-SPECIFIC GENE 2 PROTEIN


Mass: 38614.992 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN, RESIDUES 465-798
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Description: EXPRESSION SYSTEM IS PHAGE RESISTANCE ROSETTA / Cell: GERM CELL / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q8TF76, non-specific serine/threonine protein kinase

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Non-polymers , 6 types, 403 molecules

#2: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: I
#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-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 398 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Nonpolymer detailsIODIDE ION (IOD): PRODUCED BY RADIOLYTIC CLEAVAGE OF THE 5-IODOTUBERCIDIN LIGAND (2R,3R,4S,5R)-2-(4- ...IODIDE ION (IOD): PRODUCED BY RADIOLYTIC CLEAVAGE OF THE 5-IODOTUBERCIDIN LIGAND (2R,3R,4S,5R)-2-(4-AMINO-5-IODO-7H-PYRROLO[2,3- D]PYRIMIDIN-7-YL)-5-(HYDROXYMETHYL)TETRAHYDROFURAN- 3, 4-DIOL (5ID): 5-IODOTUBERCIDIN

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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: 2.62 Å3/Da / Density % sol: 61.96 % / Description: NONE
Crystal growDetails: 0.1 M SPG, 60% MPG

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9764
DetectorType: MARRESEARCH / Detector: CCD / Date: May 10, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9764 Å / Relative weight: 1
ReflectionResolution: 1.8→35.18 Å / Num. obs: 45276 / % possible obs: 97.1 % / Observed criterion σ(I): 0 / Redundancy: 3.48 % / Biso Wilson estimate: 19.5 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 5.98
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 2.49 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.18 / % possible all: 82.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: EXPERIMENTALLY PHASED STRUCTURE FROM ANOTHER CRYSTAL OF THE SAME CONSTRUCT

Resolution: 1.8→32.445 Å / SU ML: 0.16 / σ(F): 0.02 / Phase error: 16.21 / Stereochemistry target values: ML
Details: IODINE IONS AS A RESULT OF RADIOLYTIC CLEAVAGE OF THE 5-IODOTUBERCIDIN LIGAND
RfactorNum. reflection% reflection
Rfree0.1691 3548 4.4 %
Rwork0.1468 --
obs0.1478 80685 90.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.715 Å2 / ksol: 0.382 e/Å3
Displacement parametersBiso mean: 26.36 Å2
Baniso -1Baniso -2Baniso -3
1-1.3663 Å2-0 Å20 Å2
2---4.11 Å2-0 Å2
3---2.7437 Å2
Refinement stepCycle: LAST / Resolution: 1.8→32.445 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2617 0 34 398 3049
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015364
X-RAY DIFFRACTIONf_angle_d1.099674
X-RAY DIFFRACTIONf_dihedral_angle_d16.141357
X-RAY DIFFRACTIONf_chiral_restr0.1428
X-RAY DIFFRACTIONf_plane_restr0815
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.82470.2804800.26421880X-RAY DIFFRACTION55
1.8247-1.85070.2567980.26322184X-RAY DIFFRACTION64
1.8507-1.87840.2451180.22862323X-RAY DIFFRACTION68
1.8784-1.90770.20191170.21532532X-RAY DIFFRACTION75
1.9077-1.9390.1941900.20052772X-RAY DIFFRACTION81
1.939-1.97240.2591190.18842955X-RAY DIFFRACTION86
1.9724-2.00830.17321200.17363106X-RAY DIFFRACTION90
2.0083-2.04690.19241610.17583129X-RAY DIFFRACTION92
2.0469-2.08870.18341710.15533073X-RAY DIFFRACTION93
2.0887-2.13410.1791440.14663221X-RAY DIFFRACTION94
2.1341-2.18370.17571580.13783255X-RAY DIFFRACTION95
2.1837-2.23830.19971620.13233245X-RAY DIFFRACTION96
2.2383-2.29880.16361670.1243220X-RAY DIFFRACTION96
2.2988-2.36640.14991650.12783287X-RAY DIFFRACTION97
2.3664-2.44280.14771510.1253351X-RAY DIFFRACTION98
2.4428-2.53010.1571560.12253283X-RAY DIFFRACTION98
2.5301-2.63130.17331540.13283342X-RAY DIFFRACTION98
2.6313-2.7510.19111430.13793357X-RAY DIFFRACTION98
2.751-2.8960.17891190.14823389X-RAY DIFFRACTION99
2.896-3.07730.1851360.1383367X-RAY DIFFRACTION99
3.0773-3.31470.16351780.13433375X-RAY DIFFRACTION99
3.3147-3.64780.15771930.12623324X-RAY DIFFRACTION99
3.6478-4.17470.1271690.12123372X-RAY DIFFRACTION100
4.1747-5.25610.12791420.11743407X-RAY DIFFRACTION99
5.2561-32.45050.18851370.19043388X-RAY DIFFRACTION99
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)
10.308-0.00150.26030.81760.26210.29730.08960.0272-0.14930.17240.06110.02780.10390.16-0.13930.19030.0231-0.04130.17920.00140.225119.2332-25.0889-5.3541
20.6696-0.2160.36260.8033-0.12970.6902-0.0713-0.0609-0.04980.0680.0877-0.0541-0.04760.0096-0.01820.08790.0041-0.00460.1184-0.00740.089513.7969-14.4509-4.763
30.5623-0.60650.04461.5255-0.47740.29440.0051-0.04690.0086-0.04720.04140.011-0.02060.025-0.03850.014-0.00930.00830.05590.02020.0190.7011-5.9429-14.8612
40.68930.04520.08160.312-0.25541.1327-0.0839-0.23150.4580.32930.1611-0.0844-0.47540.0652-0.00390.2759-0.0019-0.02290.1599-0.06180.24233.28778.7086-5.1596
50.8088-0.80090.20711.1075-0.1660.2760.15140.13880.1728-0.2233-0.1189-0.0361-0.12190.0055-0.02530.10060.03590.01030.07490.05910.0742-1.95234.3446-23.4866
60.56530.1212-0.31240.14750.1833-0.0534-0.07740.1149-0.05940.0773-0.0983-0.0802-0.06590.04580.07640.15650.0034-0.03250.18960.02920.170411.4196-10.6381-10.7656
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESID 467:489)
2X-RAY DIFFRACTION2CHAIN A AND RESID 490:609)
3X-RAY DIFFRACTION3CHAIN A AND RESID 610:711)
4X-RAY DIFFRACTION4CHAIN A AND RESID 712:734)
5X-RAY DIFFRACTION5CHAIN A AND RESID 735:799)
6X-RAY DIFFRACTION6CHAIN B AND RESID 1:1)

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