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

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Basic information

Entry
Database: PDB / ID: 2bzh
TitleCRYSTAL STRUCTURE OF THE HUMAN PIM1 IN COMPLEX WITH A RUTHENIUM ORGANOMETALLIC LIGAND RU1
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 / : / 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 / cytosol / cytoplasm
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-1 / Serine/threonine-protein kinase pim-1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 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 1.0Dec 8, 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 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4May 8, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.5Dec 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
B: PROTO-ONCOGENE SERINE THREONINE PROTEIN KINASE PIM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2114
Polymers35,6331
Non-polymers5783
Water4,179232
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)97.529, 97.529, 80.726
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-HB1 / RUTHENIUM-PYRIDOCARBAZOLE-1


Mass: 480.438 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H13N3O3Ru
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / Source method: isolated from a natural source / Formula: H2O
Compound detailsPOSSIBLE ROLE IN SIGNAL TRANSDUCTION IN BLOOD CELLS ENGINEERED RESIDUE IN CHAIN B, ARG 250 TO GLY
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: 3.7 Å3/Da / Density % sol: 67 %
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: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Mar 4, 2005 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 34487 / % possible obs: 99.6 % / Observed criterion σ(I): 3 / Redundancy: 5.55 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.42
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.69 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 3.25 / % possible all: 97.8

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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: 1.9→40 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.961 / SU B: 4.989 / SU ML: 0.075 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.19 1751 5.1 %RANDOM
Rwork0.157 ---
obs0.159 32701 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 51.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.4 Å20.2 Å20 Å2
2--0.4 Å20 Å2
3----0.6 Å2
Refinement stepCycle: LAST / Resolution: 1.9→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2204 0 35 232 2471
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0212348
X-RAY DIFFRACTIONr_bond_other_d0.0010.022100
X-RAY DIFFRACTIONr_angle_refined_deg1.2791.9763230
X-RAY DIFFRACTIONr_angle_other_deg0.82734862
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4495284
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.94723.19116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.02615375
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8791519
X-RAY DIFFRACTIONr_chiral_restr0.0870.2342
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022619
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02518
X-RAY DIFFRACTIONr_nbd_refined0.2130.2446
X-RAY DIFFRACTIONr_nbd_other0.1830.22103
X-RAY DIFFRACTIONr_nbtor_refined0.1820.21114
X-RAY DIFFRACTIONr_nbtor_other0.0790.21313
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1220.2156
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0430.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.310.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1760.221
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.95231419
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.93352243
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.08481192
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.0511957
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: 1.9→1.95 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.303 140
Rwork0.24 2363
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)
11.9160.43451.23670.31460.10422.02990.09130.2026-0.0648-0.21990.095-0.1254-0.03170.2-0.1863-0.21910.01750.043-0.2413-0.0291-0.2176-30.5614-27.6615-0.0702
25.69095.3701-6.686435.153-9.66238.2297-0.18110.6169-0.9678-0.88650.38810.50560.6939-0.104-0.2069-0.09430.12020.0180.1930.04820.0202-22.6759-34.6987-2.7785
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B33 - 305
2X-RAY DIFFRACTION2B1307

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