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- PDB-1yxt: Crystal Structure of Kinase Pim1 in complex with AMPPNP -

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Basic information

Entry
Database: PDB / ID: 1yxt
TitleCrystal Structure of Kinase Pim1 in complex with AMPPNP
ComponentsProto-oncogene serine/threonine-protein kinase Pim-1
KeywordsTRANSFERASE / Ser/Thr protein kinase
Function / homology
Function and homology information


positive regulation of cardioblast proliferation / cellular detoxification / regulation of hematopoietic stem cell proliferation / hyaluronan metabolic process / vitamin D receptor signaling pathway / ribosomal small subunit binding / positive regulation of cyclin-dependent protein serine/threonine kinase activity / regulation of transmembrane transporter activity / protein serine/threonine kinase activator activity / positive regulation of brown fat cell differentiation ...positive regulation of cardioblast proliferation / cellular detoxification / regulation of hematopoietic stem cell proliferation / hyaluronan metabolic process / vitamin D receptor signaling pathway / ribosomal small subunit binding / positive regulation of cyclin-dependent protein serine/threonine kinase activity / regulation of transmembrane transporter activity / protein serine/threonine kinase activator activity / positive regulation of brown fat cell differentiation / positive regulation of protein serine/threonine kinase activity / positive regulation of cardiac muscle cell proliferation / negative regulation of DNA-binding transcription factor activity / manganese ion binding / protein stabilization / non-specific serine/threonine protein kinase / multicellular organism development / cell cycle / protein autophosphorylation / transcription factor binding / cytokine-mediated signaling pathway / apoptotic process / protein serine/threonine kinase activity / nucleolus / protein phosphorylation / negative regulation of apoptotic process / positive regulation of transcription, DNA-templated / nucleoplasm / ATP binding / plasma membrane / nucleus / cytosol / cytoplasm
Protein kinase domain / Protein kinase, ATP binding site / Serine/threonine-protein kinase pim-1/2/3 / Protein kinase-like domain superfamily / Serine/threonine-protein kinase, active site / Protein kinase domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 ...Protein kinase domain / Protein kinase, ATP binding site / Serine/threonine-protein kinase pim-1/2/3 / Protein kinase-like domain superfamily / Serine/threonine-protein kinase, active site / Protein kinase domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Serine/threonine-protein kinase pim-1
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKumar, A. / Mandiyan, V. / Suzuki, Y. / Zhang, C. / Rice, J. / Tsai, J. / Artis, D.R. / Ibrahim, P. / Bremer, R.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Crystal structures of proto-oncogene kinase Pim1: a target of aberrant somatic hypermutations in diffuse large cell lymphoma.
Authors: Kumar, A. / Mandiyan, V. / Suzuki, Y. / Zhang, C. / Rice, J. / Tsai, J. / Artis, D.R. / Ibrahim, P. / Bremer, R.
Validation Report
SummaryFull reportAbout validation report
History
DepositionFeb 22, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 26, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Jun 24, 2015Group: Data collection

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Proto-oncogene serine/threonine-protein kinase Pim-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3392
Polymers33,8321
Non-polymers5061
Water2,216123
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)95.566, 95.566, 80.862
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 Pim-1


Mass: 33832.320 Da / Num. of mol.: 1 / Fragment: catalytic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIM1 / Production host: Escherichia coli (E. coli) / References: UniProt: P11309, EC: 2.7.1.37
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 3.8 Å3/Da / Density % sol: 67 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Na Acetate, Imidazole, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 21, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2→82.76 Å / Num. obs: 28420 / % possible obs: 99.9 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 1.5 / Redundancy: 4.2 % / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Net I/σ(I): 11.4
Reflection shellResolution: 2→2.11 Å / % possible obs: 100 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.715 / Mean I/σ(I) obs: 1 / Num. measured obs: 4136 / Rsym value: 0.715 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMAC5.1.25refinement
PDB_EXTRACT1.6data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→81.65 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.99 / SU ML: 0.104 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 1.5 / ESU R: 0.137 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.216 1435 5.1 %RANDOM
Rwork0.181 ---
Obs0.183 26945 99.81 %-
All-28435 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 27.228 Å2
Baniso -1Baniso -2Baniso -3
1-1.24 Å20.62 Å20 Å2
2--1.24 Å20 Å2
3----1.86 Å2
Refinement stepCycle: LAST / Resolution: 2→81.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2230 0 31 123 2384
Refine LS restraints
Refinement-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0212328
X-RAY DIFFRACTIONr_bond_other_d00.022084
X-RAY DIFFRACTIONr_angle_refined_deg1.5681.9593167
X-RAY DIFFRACTIONr_angle_other_deg0.73534829
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.1785273
X-RAY DIFFRACTIONr_chiral_restr0.0940.2337
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022581
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02505
X-RAY DIFFRACTIONr_nbd_refined0.261490
X-RAY DIFFRACTIONr_nbd_other0.28712378
X-RAY DIFFRACTIONr_nbtor_other0.0850.21256
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.2137
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.33818
X-RAY DIFFRACTIONr_symmetry_vdw_other0.346146
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2990.212
X-RAY DIFFRACTIONr_mcbond_it0.7231.51366
X-RAY DIFFRACTIONr_mcangle_it1.36222215
X-RAY DIFFRACTIONr_scbond_it1.8993962
X-RAY DIFFRACTIONr_scangle_it3.1184.5952
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.334 109
Rwork0.289 2004
Refinement TLS params.Method: refined / Origin x: 65.642 Å / Origin y: 27.17 Å / Origin z: -0.747 Å
111213212223313233
T0.0843 Å2-0.0355 Å2-0.0158 Å2-0.0792 Å2-0.0378 Å2--0.1276 Å2
L2.5141 °20.2468 °2-0.4024 °2-1.7496 °2-0.0424 °2--1.7196 °2
S-0.0717 Å °0.1456 Å °0.0908 Å °-0.0718 Å °0.1087 Å °-0.0581 Å °-0.0021 Å °0.1725 Å °-0.0371 Å °
Refinement TLS groupSelection: ALL

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