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- PDB-2iwi: CRYSTAL STRUCTURE OF THE HUMAN PIM2 IN COMPLEX WITH A RUTHENIUM O... -

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Basic information

Entry
Database: PDB / ID: 2iwi
TitleCRYSTAL STRUCTURE OF THE HUMAN PIM2 IN COMPLEX WITH A RUTHENIUM ORGANOMETALLIC LIGAND RU1
ComponentsSERINE/THREONINE-PROTEIN KINASE PIM-2
KeywordsTRANSFERASE / NUCLEOTIDE-BINDING / SERINE/THREONINE-PROTEIN KINASE / PIM2 / KINASE / CANCER / LEUKEMIA / ATP-BINDING / PROTO-ONCOGENE / PHOSPHORYLATION
Function / homology
Function and homology information


apoptotic mitochondrial changes / positive regulation of macroautophagy / positive regulation of autophagy / regulation of mitotic cell cycle / macroautophagy / response to virus / G1/S transition of mitotic cell cycle / positive regulation of canonical NF-kappaB signal transduction / protein stabilization / non-specific serine/threonine protein kinase ...apoptotic mitochondrial changes / positive regulation of macroautophagy / positive regulation of autophagy / regulation of mitotic cell cycle / macroautophagy / response to virus / G1/S transition of mitotic cell cycle / positive regulation of canonical NF-kappaB signal transduction / protein stabilization / non-specific serine/threonine protein kinase / negative regulation of cell population proliferation / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / ATP binding / cytoplasm
Similarity search - Function
Serine/threonine-protein kinase pim-1/2/3 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site ...Serine/threonine-protein kinase pim-1/2/3 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / 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
RUTHENIUM-PYRIDOCARBAZOLE-1 / Serine/threonine-protein kinase pim-2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsRusso, S. / Debreczeni, J.E. / Amos, A. / Bullock, A.N. / Fedorov, O. / Niesen, F. / Sobott, F. / Turnbull, A. / Pike, A.C.W. / Ugochukwu, E. ...Russo, S. / Debreczeni, J.E. / Amos, A. / Bullock, A.N. / Fedorov, O. / Niesen, F. / Sobott, F. / Turnbull, A. / Pike, A.C.W. / Ugochukwu, E. / Papagrigoriou, E. / Bunkoczi, G. / Gorrec, F. / Edwards, A. / Arrowsmith, C. / Weigelt, J. / Sundstrom, M. / von Delft, F. / Knapp, S.
CitationJournal: PLoS ONE / Year: 2009
Title: Crystal structure of the PIM2 kinase in complex with an organoruthenium inhibitor.
Authors: Bullock, A.N. / Russo, S. / Amos, A. / Pagano, N. / Bregman, H. / Debreczeni, J.E. / Lee, W.H. / von Delft, F. / Meggers, E. / Knapp, S.
History
DepositionJun 30, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 2, 2006Provider: 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: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.4Feb 28, 2018Group: Database references / Source and taxonomy / Category: citation / entity_src_gen
Item: _citation.journal_abbrev / _citation.page_first ..._citation.journal_abbrev / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_variant
Revision 1.5May 8, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.6Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

Downloads & links

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Assembly

Deposited unit
A: SERINE/THREONINE-PROTEIN KINASE PIM-2
B: SERINE/THREONINE-PROTEIN KINASE PIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,5944
Polymers68,6332
Non-polymers9612
Water0
1
A: SERINE/THREONINE-PROTEIN KINASE PIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7972
Polymers34,3161
Non-polymers4801
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: SERINE/THREONINE-PROTEIN KINASE PIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7972
Polymers34,3161
Non-polymers4801
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)153.070, 153.070, 78.600
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1113A32 - 287
2113B32 - 287
1124A1289
2124B1289

NCS ensembles :
ID
1
2

NCS oper: (Code: given
Matrix: (0.94987, 0.28264, -0.13363), (0.29234, -0.65149, 0.70007), (0.11081, -0.70404, -0.70146)
Vector: -19.34309, 66.53331, 49.99966)

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Components

#1: Protein SERINE/THREONINE-PROTEIN KINASE PIM-2 / HUMAN PIM2 / PIM-2H


Mass: 34316.375 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star
References: UniProt: Q9P1W9, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-HB1 / RUTHENIUM-PYRIDOCARBAZOLE-1


Mass: 480.438 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H13N3O3Ru

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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: 2.63 Å3/Da / Density % sol: 53.18 %
Crystal growMethod: vapor diffusion, sitting drop
Details: 1.5 UL SITTING DROPS, 1.6 M SODIUM-POTASSIUM PHOSPHATE, 0.1 M HEPES PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9789
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 4, 2006 / Details: MIRRORS
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.8→44.19 Å / Num. obs: 16854 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.23
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.21 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1XWS

1xws


Resolution: 2.8→76.47 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.89 / SU B: 47.383 / SU ML: 0.408 / Cross valid method: THROUGHOUT / ESU R: 1.485 / ESU R Free: 0.402 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.289 834 5 %RANDOM
Rwork0.242 ---
obs0.244 15818 98.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.47 Å2
Baniso -1Baniso -2Baniso -3
1--5.73 Å2-2.87 Å20 Å2
2---5.73 Å20 Å2
3---8.6 Å2
Refinement stepCycle: LAST / Resolution: 2.8→76.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3686 0 60 0 3746
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223872
X-RAY DIFFRACTIONr_bond_other_d0.0020.022545
X-RAY DIFFRACTIONr_angle_refined_deg1.2652.0015352
X-RAY DIFFRACTIONr_angle_other_deg0.92336191
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8465488
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.222.886149
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.29615538
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1791523
X-RAY DIFFRACTIONr_chiral_restr0.0730.2588
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024331
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02805
X-RAY DIFFRACTIONr_nbd_refined0.2210.2981
X-RAY DIFFRACTIONr_nbd_other0.1910.22585
X-RAY DIFFRACTIONr_nbtor_refined0.1870.21931
X-RAY DIFFRACTIONr_nbtor_other0.0880.21992
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.295
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1410.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2290.225
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_it0.4231.52508
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.69923919
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.79331815
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.2564.51382
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1374tight positional0.040.05
21A43medium positional0.030.5
22B43medium positional0.030.5
11A1543loose positional0.425
11A1374tight thermal2.9115
21A43medium thermal1.812
22B43medium thermal1.812
11A1543loose thermal3.1415
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.422 60
Rwork0.336 1163

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