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- PDB-5cem: Pseudokinase and C-terminal extension of Human Tribbles Homolog 1 -

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Basic information

Entry
Database: PDB / ID: 5cem
TitlePseudokinase and C-terminal extension of Human Tribbles Homolog 1
ComponentsTribbles homolog 1
KeywordsTRANSFERASE / Kinase / Kinase-like
Function / homology
Function and homology information


ubiquitin-protein transferase regulator activity / positive regulation of eosinophil differentiation / negative regulation of smooth muscle cell migration / regulation of MAP kinase activity / negative regulation of neutrophil differentiation / positive regulation of macrophage differentiation / negative regulation of lipopolysaccharide-mediated signaling pathway / NGF-stimulated transcription / mitogen-activated protein kinase kinase binding / protein kinase inhibitor activity ...ubiquitin-protein transferase regulator activity / positive regulation of eosinophil differentiation / negative regulation of smooth muscle cell migration / regulation of MAP kinase activity / negative regulation of neutrophil differentiation / positive regulation of macrophage differentiation / negative regulation of lipopolysaccharide-mediated signaling pathway / NGF-stimulated transcription / mitogen-activated protein kinase kinase binding / protein kinase inhibitor activity / JNK cascade / negative regulation of smooth muscle cell proliferation / negative regulation of protein kinase activity / negative regulation of DNA-binding transcription factor activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / RNA polymerase II-specific DNA-binding transcription factor binding / response to lipopolysaccharide / ubiquitin protein ligase binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Tribbles homologue 1 / Pseudokinase tribbles family/serine-threonine-protein kinase 40 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain ...Tribbles homologue 1 / Pseudokinase tribbles family/serine-threonine-protein kinase 40 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å
AuthorsMace, P.D. / Nakatani, Y.
CitationJournal: Structure / Year: 2015
Title: Molecular Mechanism of CCAAT-Enhancer Binding Protein Recruitment by the TRIB1 Pseudokinase.
Authors: Murphy, J.M. / Nakatani, Y. / Jamieson, S.A. / Dai, W. / Lucet, I.S. / Mace, P.D.
History
DepositionJul 7, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2015Group: Database references
Revision 1.2Nov 1, 2017Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations
Category: citation / diffrn_source ...citation / diffrn_source / pdbx_struct_assembly_auth_evidence / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tribbles homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5485
Polymers33,1641
Non-polymers3844
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.384, 81.384, 85.883
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Detailsauthors have used SAXS

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Components

#1: Protein Tribbles homolog 1 / TRB-1 / G-protein-coupled receptor-induced gene 2 protein / GIG-2 / SKIP1


Mass: 33163.824 Da / Num. of mol.: 1 / Fragment: unp residues 83-371
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRIB1, C8FW, GIG2, TRB1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q96RU8
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.32 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: 1.0 M Ammonium sulfate, 0.1 M Bis-Tris (pH 5.5), 1% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: May 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.1→42.9 Å / Num. obs: 18911 / % possible obs: 100 % / Redundancy: 20 % / Net I/σ(I): 21.3
Reflection shellResolution: 2.1→2.21 Å / Mean I/σ(I) obs: 3.2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementResolution: 2.1→42.9 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.936 / SU B: 9.605 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.185 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22299 1031 5.5 %RANDOM
Rwork0.17613 ---
obs0.17862 17853 99.9 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.487 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20.04 Å20 Å2
2--0.07 Å2-0 Å2
3----0.23 Å2
Refinement stepCycle: 1 / Resolution: 2.1→42.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2043 0 20 107 2170
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192127
X-RAY DIFFRACTIONr_bond_other_d0.0030.022062
X-RAY DIFFRACTIONr_angle_refined_deg1.3851.9832878
X-RAY DIFFRACTIONr_angle_other_deg0.92334743
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0825254
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.2621.73598
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.58415379
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4351524
X-RAY DIFFRACTIONr_chiral_restr0.0790.2321
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212310
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02498
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
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_it4.2092.6391010
X-RAY DIFFRACTIONr_mcbond_other4.212.6381009
X-RAY DIFFRACTIONr_mcangle_it5.9533.9161257
X-RAY DIFFRACTIONr_mcangle_other5.9513.9191258
X-RAY DIFFRACTIONr_scbond_it5.2553.161117
X-RAY DIFFRACTIONr_scbond_other5.1663.1051099
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.3944.4621594
X-RAY DIFFRACTIONr_long_range_B_refined9.9821.3292366
X-RAY DIFFRACTIONr_long_range_B_other9.73120.9732324
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.101→2.156 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 70 -
Rwork0.247 1330 -
obs--99.22 %
Refinement TLS params.Method: refined / Origin x: 30.204 Å / Origin y: 46.806 Å / Origin z: 0.6 Å
111213212223313233
T0.02 Å2-0.0033 Å2-0.005 Å2-0.0352 Å2-0.0111 Å2--0.0889 Å2
L3.2207 °2-0.3044 °2-0.7409 °2-0.3961 °20.0798 °2--0.6085 °2
S-0.0659 Å °0.1903 Å °-0.0983 Å °-0.0436 Å °0.0227 Å °-0.0176 Å °0.0146 Å °0.0423 Å °0.0432 Å °

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