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- PDB-2pom: TAB1 with manganese ion -

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Basic information

Entry
Database: PDB / ID: 2pom
TitleTAB1 with manganese ion
ComponentsMitogen-activated protein kinase kinase kinase 7-interacting protein 1
KeywordsSIGNALING PROTEIN/METAL BINDING PROTEIN / pp2c-like domain / SIGNALING PROTEIN-METAL BINDING PROTEIN COMPLEX
Function / homology
Function and homology information


cardiac septum development / coronary vasculature development / aorta development / protein serine/threonine phosphatase activity / mitogen-activated protein kinase p38 binding / non-canonical NF-kappaB signal transduction / enzyme activator activity / heart morphogenesis / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway ...cardiac septum development / coronary vasculature development / aorta development / protein serine/threonine phosphatase activity / mitogen-activated protein kinase p38 binding / non-canonical NF-kappaB signal transduction / enzyme activator activity / heart morphogenesis / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / TICAM1,TRAF6-dependent induction of TAK1 complex / TRAF6-mediated induction of TAK1 complex within TLR4 complex / protein serine/threonine kinase activator activity / transforming growth factor beta receptor signaling pathway / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / TNFR1-induced NF-kappa-B signaling pathway / activated TAK1 mediates p38 MAPK activation / lung development / TAK1-dependent IKK and NF-kappa-B activation / NOD1/2 Signaling Pathway / positive regulation of protein serine/threonine kinase activity / CLEC7A (Dectin-1) signaling / FCERI mediated NF-kB activation / Interleukin-1 signaling / in utero embryonic development / positive regulation of MAPK cascade / molecular adaptor activity / endosome membrane / Ub-specific processing proteases / nuclear speck / protein-containing complex binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / endoplasmic reticulum / protein-containing complex / cytosol / cytoplasm
Similarity search - Function
PPM-type phosphatase domain / Phosphatase 2c; domain 1 / Protein phosphatase 2C / Protein phosphatase 2C family / Serine/threonine phosphatases, family 2C, catalytic domain / PPM-type phosphatase domain profile. / PPM-type phosphatase-like domain / PPM-type phosphatase-like domain superfamily / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / TGF-beta-activated kinase 1 and MAP3K7-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsLin, S.C.
CitationJournal: Mol.Cell / Year: 2007
Title: XIAP Induces NF-kappaB Activation via the BIR1/TAB1 Interaction and BIR1 Dimerization.
Authors: Lu, M. / Lin, S.C. / Huang, Y. / Kang, Y.J. / Rich, R. / Lo, Y.C. / Myszka, D. / Han, J. / Wu, H.
History
DepositionApr 26, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mitogen-activated protein kinase kinase kinase 7-interacting protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8422
Polymers40,7871
Non-polymers551
Water27015
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)141.618, 141.618, 66.153
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
DetailsThe biological assembly is a monomer.

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Components

#1: Protein Mitogen-activated protein kinase kinase kinase 7-interacting protein 1 / TGF-beta-activated kinase 1-binding protein 1 / TAK1-binding protein 1


Mass: 40786.797 Da / Num. of mol.: 1 / Fragment: N-TERMINAL PP2C-LIKE DOMAIN, RESIDUES 1-370
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAP3K7IP1, TAB1 / Plasmid: pGEX-4T3 / Species (production host): Escherichia coli / Production host: Escherichia coli K12 (bacteria) / Strain (production host): K-12 / References: UniProt: Q15750
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 4.71 Å3/Da / Density % sol: 73.89 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.5M Li2SO4, 0.1M Hepes, 1mM MnCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 213 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97919 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 6, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 2.22→50 Å / Num. obs: 35865 / % possible obs: 95 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.069 / Χ2: 1.159 / Net I/σ(I): 13.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.22-2.263.60.45913120.91171
2.26-2.33.80.40714500.7976.9
2.3-2.344.20.39814900.71880.7
2.34-2.394.40.38816390.70886.7
2.39-2.444.80.34517430.71193
2.44-2.55.10.34717950.65397.3
2.5-2.565.60.31618940.71299.5
2.56-2.636.30.27718560.73299.9
2.63-2.716.70.27718750.76100
2.71-2.870.2318630.757100
2.8-2.97.10.16819070.84100
2.9-3.017.10.13118760.91999.9
3.01-3.157.20.10818891.09699.9
3.15-3.327.20.08618851.293100
3.32-3.527.20.07218881.55999.9
3.52-3.87.20.06218881.623100
3.8-4.187.10.05818911.82100
4.18-4.7870.04819191.69699.6
4.78-6.026.80.04319251.67599.9
6.02-506.50.03718801.77993.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: The TAB1 model solved by ourselves, but Not deposited yet

Resolution: 2.27→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.233 2593 7.3 %random
Rwork0.211 ---
obs-32075 90.3 %-
Solvent computationBsol: 44.339 Å2
Displacement parametersBiso mean: 56.886 Å2
Baniso -1Baniso -2Baniso -3
1--7.398 Å2-7.776 Å20 Å2
2---7.398 Å20 Å2
3---14.796 Å2
Refinement stepCycle: LAST / Resolution: 2.27→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2736 0 1 15 2752
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obs
2.27-2.370.442190.397X-RAY DIFFRACTION2867
2.37-2.50.3562820.326X-RAY DIFFRACTION3465
2.5-2.650.3133440.269X-RAY DIFFRACTION3993
2.65-2.860.2643280.245X-RAY DIFFRACTION4135
2.86-3.150.2813730.243X-RAY DIFFRACTION4299
3.15-3.60.2573670.226X-RAY DIFFRACTION4388
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:ion.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param

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