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- PDB-2bzj: CRYSTAL STRUCTURE OF THE HUMAN PIM1 IN COMPLEX WITH A RUTHENIUM O... -

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Basic information

Entry
Database: PDB / ID: 2bzj
TitleCRYSTAL STRUCTURE OF THE HUMAN PIM1 IN COMPLEX WITH A RUTHENIUM ORGANOMETALLIC LIGAND RU3
ComponentsPROTO-ONCOGENE SERINE THREONINE PROTEIN KINASE PIM1
KeywordsTRANSFERASE / PIM1 / KINASE / CANCER / LEUKEMIA / NUCLEAR PROTEIN / NUCLEOTIDE-BINDING
Function / homology
Function and homology information


positive regulation of cardioblast proliferation / positive regulation of cyclin-dependent protein serine/threonine kinase activity / regulation of transmembrane transporter activity / regulation of hematopoietic stem cell proliferation / vitamin D receptor signaling pathway / cellular detoxification / STAT5 activation downstream of FLT3 ITD mutants / transcription factor binding / ribosomal small subunit binding / positive regulation of protein serine/threonine kinase activity ...positive regulation of cardioblast proliferation / positive regulation of cyclin-dependent protein serine/threonine kinase activity / regulation of transmembrane transporter activity / regulation of hematopoietic stem cell proliferation / vitamin D receptor signaling pathway / cellular detoxification / STAT5 activation downstream of FLT3 ITD mutants / transcription factor binding / ribosomal small subunit binding / positive regulation of protein serine/threonine kinase activity / negative regulation of DNA-binding transcription factor activity / positive regulation of cardiac muscle cell proliferation / positive regulation of brown fat cell differentiation / Signaling by FLT3 fusion proteins / positive regulation of TORC1 signaling / regulation of mitotic cell cycle / negative regulation of innate immune response / protein serine/threonine kinase activator activity / cellular response to type II interferon / manganese ion binding / protein autophosphorylation / Interleukin-4 and Interleukin-13 signaling / protein phosphorylation / non-specific serine/threonine protein kinase / protein stabilization / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / nucleolus / nucleoplasm / ATP binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Serine/threonine-protein kinase pim-1/2/3 / : / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain ...Serine/threonine-protein kinase pim-1/2/3 / : / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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-3 / Serine/threonine-protein kinase pim-1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsDebreczeni, J.E. / Bullock, A. / Knapp, S. / von Delft, F. / Sundstrom, M. / Arrowsmith, C. / Weigelt, J. / Edwards, A.
CitationJournal: To be Published
Title: Crystal Structure of the Human Pim1 in Complex with Ruthenium Organometallic Ligands
Authors: Debreczeni, J.E. / Bullock, A. / Knapp, S. / von Delft, F. / Sundstrom, M. / Arrowsmith, C. / Weigelt, J. / Edwards, A.
History
DepositionAug 18, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 12, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTO-ONCOGENE SERINE THREONINE PROTEIN KINASE PIM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2022
Polymers35,6331
Non-polymers5701
Water2,522140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)98.887, 98.887, 81.028
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein PROTO-ONCOGENE SERINE THREONINE PROTEIN KINASE PIM1


Mass: 35632.602 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: ISOFORM MUTATION R250G / Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: P11-TORONTO / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P11309, EC: 2.7.1.37
#2: Chemical ChemComp-ME3 / RUTHENIUM-PYRIDOCARBAZOLE-3


Mass: 569.508 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H18N3O6Ru
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ARG 250 TO GLY MAY PLAY A ROLE IN SIGNAL TRANSDUCTION IN BLOOD CELLS.
Sequence detailsISOFORM MUTATION R250G

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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: 3.4 Å3/Da / Density % sol: 63.52 %
Crystal growMethod: vapor diffusion, sitting drop
Details: 0.1 M SUCCINATE PHOSPHATE GLYCINE BUFFER PH 6, 30% PEG1K, 0.5% DMSO, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.978
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 23, 2005 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 27388 / % possible obs: 96.7 % / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.4
Reflection shellResolution: 2.05→2.15 Å / Redundancy: 2 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2 / % possible all: 80

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1XWS

1xws


Resolution: 2.05→85.75 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.94 / SU B: 8.354 / SU ML: 0.118 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.148 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.221 1381 5.1 %RANDOM
Rwork0.183 ---
obs0.185 25947 96.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.77 Å2
Baniso -1Baniso -2Baniso -3
1-0.61 Å20.31 Å20 Å2
2--0.61 Å20 Å2
3----0.92 Å2
Refinement stepCycle: LAST / Resolution: 2.05→85.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2213 0 36 140 2389
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0212334
X-RAY DIFFRACTIONr_bond_other_d0.0010.022087
X-RAY DIFFRACTIONr_angle_refined_deg1.391.9813204
X-RAY DIFFRACTIONr_angle_other_deg0.84634831
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4755272
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.7823.136118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.71715382
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4991521
X-RAY DIFFRACTIONr_chiral_restr0.0740.2334
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022579
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02503
X-RAY DIFFRACTIONr_nbd_refined0.1840.2424
X-RAY DIFFRACTIONr_nbd_other0.180.22022
X-RAY DIFFRACTIONr_nbtor_refined0.1760.21082
X-RAY DIFFRACTIONr_nbtor_other0.0810.21273
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2133
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0530.22
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3140.231
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1320.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9191.51506
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.36422206
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.62631229
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.6154.5971
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
LS refinement shellResolution: 2.05→2.1 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.452 63
Rwork0.328 1444
Refinement TLS params.Method: refined / Origin x: -31.164 Å / Origin y: -27.673 Å / Origin z: 2.123 Å
111213212223313233
T-0.0072 Å20.011 Å20.0241 Å2--0.0517 Å2-0.0248 Å2---0.0945 Å2
L1.6117 °2-0.4605 °20.4545 °2-1.0779 °2-0.0068 °2--1.0063 °2
S-0.0149 Å °-0.0339 Å °-0.0756 Å °-0.0514 Å °0.103 Å °-0.0442 Å °-0.0179 Å °0.0834 Å °-0.088 Å °

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