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- PDB-7vsy: Pim1 with N82K mutation -

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Basic information

Entry
Database: PDB / ID: 7vsy
TitlePim1 with N82K mutation
ComponentsSerine/threonine-protein kinase pim-1
KeywordsONCOPROTEIN / Kinase / activity / point mutation / catalytic domain
Function / homology
Function and homology information


positive regulation of cardioblast proliferation / regulation of hematopoietic stem cell proliferation / cellular detoxification / vitamin D receptor signaling pathway / STAT5 activation downstream of FLT3 ITD mutants / transcription factor binding / positive regulation of cyclin-dependent protein serine/threonine kinase activity / ribosomal small subunit binding / positive regulation of cardiac muscle cell proliferation / positive regulation of TORC1 signaling ...positive regulation of cardioblast proliferation / regulation of hematopoietic stem cell proliferation / cellular detoxification / vitamin D receptor signaling pathway / STAT5 activation downstream of FLT3 ITD mutants / transcription factor binding / positive regulation of cyclin-dependent protein serine/threonine kinase activity / ribosomal small subunit binding / positive regulation of cardiac muscle cell proliferation / positive regulation of TORC1 signaling / Signaling by FLT3 fusion proteins / negative regulation of innate immune response / positive regulation of brown fat cell differentiation / protein serine/threonine kinase activator activity / regulation of transmembrane transporter activity / positive regulation of protein serine/threonine kinase activity / negative regulation of DNA-binding transcription factor activity / cellular response to type II interferon / manganese ion binding / Interleukin-4 and Interleukin-13 signaling / protein autophosphorylation / protein stabilization / non-specific serine/threonine protein kinase / cell cycle / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / nucleolus / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / nucleoplasm / ATP binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Serine/threonine-protein kinase pim-1/2/3 / 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
Similarity search - Domain/homology
Serine/threonine-protein kinase pim-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.141 Å
AuthorsHsu, C.Y. / Tzeng, S.R.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Other government Taiwan
CitationJournal: To Be Published
Title: Pim1 with N82K mutation
Authors: Hsu, C.Y. / Tzeng, S.R.
History
DepositionOct 27, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 27, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein kinase pim-1


Theoretical massNumber of molelcules
Total (without water)37,3081
Polymers37,3081
Non-polymers00
Water1,20767
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, HiLoad 16/600 Superdex 75 pg (GE Healthcare)
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.673, 97.673, 80.499
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: -x,-y,z+1/2

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Components

#1: Protein Serine/threonine-protein kinase pim-1


Mass: 37308.488 Da / Num. of mol.: 1 / Mutation: N82K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIM1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P11309
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O

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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: 2.97 Å3/Da / Density % sol: 58.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7.5 / Details: Na.HEPES, NaCl / PH range: 7.3-7.6

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 13, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.14→30 Å / Num. obs: 24119 / % possible obs: 100 % / Redundancy: 11 % / Biso Wilson estimate: 47.17 Å2 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.02 / Rrim(I) all: 0.065 / Χ2: 0.964 / Net I/σ(I): 14 / Num. measured all: 265143
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.14-2.229.91.06724030.8610.3561.1250.77100
2.22-2.31110.91723960.9050.290.9621.079100
2.31-2.4111.30.53323840.9620.1660.5590.837100
2.41-2.5411.30.3924050.9730.1210.4090.917100
2.54-2.711.20.26923990.9870.0840.2820.996100
2.7-2.911.20.14724020.9960.0460.1540.98100
2.9-3.211.20.08324190.9980.0260.0871.178100
3.2-3.6611.20.04824170.9990.0150.0511.053100
3.66-4.6111.10.033242710.010.0350.949100
4.61-3010.60.03524670.9990.0110.0370.8599.6

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.141→25.034 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2202 2010 8.35 %
Rwork0.1963 22057 -
obs0.1983 24067 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 93.55 Å2 / Biso mean: 53.9163 Å2 / Biso min: 33.76 Å2
Refinement stepCycle: final / Resolution: 2.141→25.034 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2200 0 0 67 2267
Biso mean---52.45 -
Num. residues----273
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112259
X-RAY DIFFRACTIONf_angle_d1.1583060
X-RAY DIFFRACTIONf_chiral_restr0.077330
X-RAY DIFFRACTIONf_plane_restr0.006393
X-RAY DIFFRACTIONf_dihedral_angle_d5.5031338
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.1412-2.19470.26761390.27221545
2.1947-2.2540.32291450.28891579
2.254-2.32030.28481400.2571568
2.3203-2.39520.26971430.23271560
2.3952-2.48070.30941430.24031571
2.4807-2.57990.26331440.2421592
2.5799-2.69720.27851400.24581548
2.6972-2.83920.28611450.24851563
2.8392-3.01680.28031480.24041588
3.0168-3.24930.24341440.22941582
3.2493-3.57550.221410.19351559
3.5755-4.09090.20811460.16751596
4.0909-5.14670.15271420.15191591
5.1467-25.0340.19291500.17281615

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