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- PDB-5cek: Pseudokinase domain of Human Tribbles Homolog 1 -

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Basic information

Entry
Database: PDB / ID: 5cek
TitlePseudokinase domain of Human Tribbles Homolog 1
ComponentsTribbles homolog 1
KeywordsTRANSFERASE / kinase
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: 2.8 Å
AuthorsMace, P.D. / Nakatani, Y.
Funding support New Zealand, 2items
OrganizationGrant numberCountry
Royal Society of New Zealand New Zealand
Health Research Council (HRC) New Zealand
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 1.2Sep 20, 2017Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 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


Theoretical massNumber of molelcules
Total (without water)29,9561
Polymers29,9561
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)152.693, 152.693, 62.798
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

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


Mass: 29955.529 Da / Num. of mol.: 1 / Fragment: unp residues 83-343
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

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.53 Å3/Da / Density % sol: 65.13 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M Bis-Tris, 2-3 M NaCl, 0.1 M Sodium Citrate and 0.01 M reduced L-Glutathione, 0.01 M oxidized L-Glutathione

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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: 2.8→48.5 Å / Num. obs: 11093 / % possible obs: 100 % / Redundancy: 9.6 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 18.6
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 9.9 % / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
XDSdata reduction
SCALAdata scaling
SHELXDEphasing
RefinementResolution: 2.8→48.5 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.938 / SU B: 39.215 / SU ML: 0.299 / Cross valid method: THROUGHOUT / ESU R: 0.489 / ESU R Free: 0.3 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24554 590 5.3 %RANDOM
Rwork0.20736 ---
obs0.20937 10489 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 100.759 Å2
Baniso -1Baniso -2Baniso -3
1-2.12 Å21.06 Å2-0 Å2
2--2.12 Å2-0 Å2
3----6.88 Å2
Refinement stepCycle: 1 / Resolution: 2.8→48.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1919 0 0 0 1919
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0191962
X-RAY DIFFRACTIONr_bond_other_d0.0020.021926
X-RAY DIFFRACTIONr_angle_refined_deg1.3761.9712647
X-RAY DIFFRACTIONr_angle_other_deg0.98234423
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3565232
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.47721.49487
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.76915349
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6541521
X-RAY DIFFRACTIONr_chiral_restr0.0710.2298
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212119
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02462
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_it5.5255.64943
X-RAY DIFFRACTIONr_mcbond_other5.5225.639942
X-RAY DIFFRACTIONr_mcangle_it7.9218.441170
X-RAY DIFFRACTIONr_mcangle_other7.9188.4411171
X-RAY DIFFRACTIONr_scbond_it6.356.3371019
X-RAY DIFFRACTIONr_scbond_other6.3466.3371020
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.4819.2581478
X-RAY DIFFRACTIONr_long_range_B_refined13.47754.5637948
X-RAY DIFFRACTIONr_long_range_B_other13.47654.5647949
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.403 47 -
Rwork0.327 750 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -33.661 Å / Origin y: 36.677 Å / Origin z: -0.76 Å
111213212223313233
T0.3624 Å2-0.1539 Å2-0.0023 Å2-0.0841 Å2-0.0419 Å2--0.2055 Å2
L2.4209 °2-0.2853 °20.2204 °2-5.7178 °2-2.3697 °2--5.4594 °2
S0.1563 Å °-0.1638 Å °0.5347 Å °0.8336 Å °-0.1235 Å °-0.522 Å °0.1863 Å °-0.2869 Å °-0.0329 Å °

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