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- PDB-4g3g: Crystal structure of murine NF-kappaB inducing kinase (NIK) V408L... -

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Basic information

Entry
Database: PDB / ID: 4g3g
TitleCrystal structure of murine NF-kappaB inducing kinase (NIK) V408L bound to a 2-(aminothiazolyl)phenol (cmp3)
ComponentsNF-kappa-beta-inducing kinase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / non-RD kinase / protein serine/threonine kinase / NF-kappaB / MAP3K14 / Structure-based drug design / transferase / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


CD28 dependent PI3K/Akt signaling / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / Dectin-1 mediated noncanonical NF-kB signaling / NIK-->noncanonical NF-kB signaling / TNFR2 non-canonical NF-kB pathway / mitogen-activated protein kinase kinase kinase / non-canonical NF-kappaB signal transduction / MAP kinase kinase kinase activity / canonical NF-kappaB signal transduction / fibrillar center ...CD28 dependent PI3K/Akt signaling / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / Dectin-1 mediated noncanonical NF-kB signaling / NIK-->noncanonical NF-kB signaling / TNFR2 non-canonical NF-kB pathway / mitogen-activated protein kinase kinase kinase / non-canonical NF-kappaB signal transduction / MAP kinase kinase kinase activity / canonical NF-kappaB signal transduction / fibrillar center / cellular response to mechanical stimulus / defense response to virus / protein kinase activity / immune response / phosphorylation / protein serine kinase activity / intracellular membrane-bounded organelle / protein serine/threonine kinase activity / nucleoplasm / ATP binding / cytosol
Similarity search - Function
Mitogen-activated protein (MAP) kinase kinase kinase 14 / M3K14, catalytic domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain ...Mitogen-activated protein (MAP) kinase kinase kinase 14 / M3K14, catalytic domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-0WA / Mitogen-activated protein kinase kinase kinase 14
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsHymowitz, S.
CitationJournal: Structure / Year: 2012
Title: The crystal structure of the catalytic domain of the NF-kappaB inducing kinase reveals a narrow but flexible active site.
Authors: de Leon-Boenig, G. / Bowman, K.K. / Feng, J.A. / Crawford, T. / Everett, C. / Franke, Y. / Oh, A. / Stanley, M. / Staben, S.T. / Starovasnik, M.A. / Wallweber, H.J. / Wu, J. / Wu, L.C. / ...Authors: de Leon-Boenig, G. / Bowman, K.K. / Feng, J.A. / Crawford, T. / Everett, C. / Franke, Y. / Oh, A. / Stanley, M. / Staben, S.T. / Starovasnik, M.A. / Wallweber, H.J. / Wu, J. / Wu, L.C. / Johnson, A.R. / Hymowitz, S.G.
History
DepositionJul 13, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / software / 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 / _software.name / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NF-kappa-beta-inducing kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0932
Polymers38,8061
Non-polymers2871
Water68538
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.423, 135.320, 64.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-822-

HOH

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Components

#1: Protein NF-kappa-beta-inducing kinase / Serine/threonine-protein kinase NIK


Mass: 38805.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Map3k14, NF-kappaB inducing kinase (NIK), Nik / Plasmid: pAcGP67 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9
References: UniProt: Q9WUL6, mitogen-activated protein kinase kinase kinase
#2: Chemical ChemComp-0WA / 4-fluoro-2-{[4-(pyridin-4-yl)-1,3-thiazol-2-yl]amino}phenol


Mass: 287.312 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H10FN3OS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 2.08 Å3/Da / Density % sol: 40.99 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 uL protein plus 0.2 uL of 0.5 mM Cmp3, 100 mM HEPES pH 7.0, 0.01 M zinc chloride, 20% PEG 6000, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.97946 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 13, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.5→46.57 Å / Num. all: 11486 / Num. obs: 11486 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Rsym value: 0.119 / Net I/σ(I): 15.6
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 1.8 / Num. unique all: 1051 / Rsym value: 0.619 / % possible all: 93.3

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Processing

Software
NameVersionClassification
Web-Icedata collection
PHASERphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→46.57 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.905 / SU B: 19.01 / SU ML: 0.209 / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R: 1.69 / ESU R Free: 0.323 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2515 1143 10 %RANDOM
Rwork0.19589 ---
all0.20136 11472 --
obs0.20136 10329 99.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.35 Å2
Baniso -1Baniso -2Baniso -3
1-1.58 Å20 Å2-0 Å2
2---1.06 Å20 Å2
3----0.51 Å2
Refinement stepCycle: LAST / Resolution: 2.5→46.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2421 0 20 38 2479
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0192554
X-RAY DIFFRACTIONr_angle_refined_deg1.1951.9813460
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4265321
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.57823.028109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.91815445
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7721521
X-RAY DIFFRACTIONr_chiral_restr0.0830.2364
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211948
LS refinement shellResolution: 2.5→2.552 Å / Total num. of bins used: 25
RfactorNum. reflection% reflection
Rfree0.357 62 -
Rwork0.283 478 -
obs--86.96 %
Refinement TLS params.Method: refined / Origin x: 18.7916 Å / Origin y: 17.6438 Å / Origin z: 2.4961 Å
111213212223313233
T0.0143 Å2-0.0029 Å20.0083 Å2-0.0617 Å2-0.0133 Å2--0.0461 Å2
L0.6051 °20.2004 °20.0736 °2-2.2126 °2-0.4455 °2--1.5469 °2
S-0.0358 Å °-0.0242 Å °-0.0041 Å °-0.003 Å °0.0129 Å °0.1264 Å °0.125 Å °-0.0392 Å °0.0229 Å °

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