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- PDB-3rzf: Crystal Structure of Inhibitor of kappaB kinase beta (I4122) -

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Basic information

Entry
Database: PDB / ID: 3rzf
TitleCrystal Structure of Inhibitor of kappaB kinase beta (I4122)
ComponentsMGC80376 protein
KeywordsIMMUNE SYSTEM / SIGNALING PROTEIN / kinase uld / kinase ubiquitin-like domain scaffold helix / kinase / I kappa B alpha / phosphorylation
Function / homology
Function and homology information


IkappaB kinase / IkappaB kinase activity / ATP binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #250 / I-kappa-kinase-beta NEMO binding domain / IKBKB, scaffold dimerization domain / IKBKB, scaffold dimerization domain superfamily / I-kappa-kinase-beta NEMO binding domain / IQBAL scaffold dimerization domain / I-kappa-kinase-beta NEMO binding domain / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) ...Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #250 / I-kappa-kinase-beta NEMO binding domain / IKBKB, scaffold dimerization domain / IKBKB, scaffold dimerization domain superfamily / I-kappa-kinase-beta NEMO binding domain / IQBAL scaffold dimerization domain / I-kappa-kinase-beta NEMO binding domain / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Roll / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Up-down Bundle / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-XNM / IkappaB kinase
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 4 Å
AuthorsXu, G. / Lo, Y.C. / Li, Q. / Napolitano, G. / Wu, X. / Jiang, X. / Dreano, M. / Karin, M. / Wu, H.
CitationJournal: Nature / Year: 2011
Title: Crystal structure of inhibitor of KappaB kinase Beta.
Authors: Xu, G. / Lo, Y.C. / Li, Q. / Napolitano, G. / Wu, X. / Jiang, X. / Dreano, M. / Karin, M. / Wu, H.
History
DepositionMay 11, 2011Deposition site: RCSB / Processing site: RCSB
SupersessionMay 25, 2011ID: 3QAD
Revision 1.0May 25, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 28, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MGC80376 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,4392
Polymers78,0021
Non-polymers4381
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)164.656, 164.656, 273.458
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein MGC80376 protein


Mass: 78001.508 Da / Num. of mol.: 1 / Mutation: S177E, S181E / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: Q6INT1
#2: Chemical ChemComp-XNM / (4-{[4-(4-chlorophenyl)pyrimidin-2-yl]amino}phenyl)[4-(2-hydroxyethyl)piperazin-1-yl]methanone


Mass: 437.922 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H24ClN5O2

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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: 5.94 Å3/Da / Density % sol: 79.29 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 5.6
Details: 1.8M K/Na phosphate, pH 5.6, VAPOR DIFFUSION, temperature 277K

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Data collection

DiffractionMean temperature: 83 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.963937, 0.979163, 0.979328
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 8, 2010
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9639371
20.9791631
30.9793281
ReflectionResolution: 4→30 Å / Num. obs: 13319 / % possible obs: 97.3 % / Observed criterion σ(F): 1.2 / Observed criterion σ(I): 2 / Redundancy: 6.9 % / Biso Wilson estimate: 130 Å2 / Rmerge(I) obs: 0.056 / Rsym value: 0.078 / Net I/σ(I): 25.3
Reflection shellResolution: 4→4.3021 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.056 / Mean I/σ(I) obs: 25.3 / Num. unique all: 12469 / Rsym value: 0.078 / % possible all: 97.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHARPphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 4→14.965 Å / SU ML: 0.72 / σ(F): 0 / Phase error: 42.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3399 655 4.92 %5%
Rwork0.2699 ---
obs0.2732 13319 83.69 %-
all-15817 --
Solvent computationShrinkage radii: 0.49 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 200.529 Å2 / ksol: 0.184 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-40.2013 Å20 Å2-0 Å2
2--40.2013 Å2-0 Å2
3----80.4026 Å2
Refinement stepCycle: LAST / Resolution: 4→14.965 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4368 0 31 0 4399
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0484579
X-RAY DIFFRACTIONf_angle_d1.7476060
X-RAY DIFFRACTIONf_dihedral_angle_d20.5091735
X-RAY DIFFRACTIONf_chiral_restr0.106677
X-RAY DIFFRACTIONf_plane_restr0.006778
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4-4.30210.50851040.40221918X-RAY DIFFRACTION65
4.3021-4.72260.37941200.32442234X-RAY DIFFRACTION75
4.7226-5.3780.43941120.32732534X-RAY DIFFRACTION84
5.378-6.67420.39531530.30862882X-RAY DIFFRACTION94
6.6742-14.96510.27421660.21173096X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.31210.8372-1.4954-0.3815-0.32430.48640.98841.1770.69020.80010.2754-0.5983-0.4041-0.37161.44860.9916-0.25460.02131.8687-0.16131.854596.4567-33.291560.0335
23.9022-1.96570.6876.76621.60111.0747-0.4279-0.5895-0.22991.08361.0332-0.8617-0.09730.82110.64650.8707-0.62670.16361.809-0.37631.1379.3564-30.823652.6644
32.1442-0.8008-0.45392.54551.9499-0.20951.102-0.2096-0.26352.2229-0.6869-0.39370.6979-0.01890.02430.7671-0.19440.3161.1675-0.21960.836664.5919-28.444750.4089
41.96310.0995-0.79984.2094-0.74520.6432-0.26251.61450.6327-2.04220.52040.3516-0.42561.2967-01.5755-0.01890.03311.6407-0.03631.237564.9827-21.36318.0643
51.1158-0.2673-2.0512.0885-1.2354.0232-0.4518-1.37930.62460.2444-0.2114-0.3448-0.83443.8551-0.09611.27820.41170.6019-0.6151-0.54191.19363.0529-5.276243.8078
60.07430.62110.08060.75070.20890.1226-1.2582.706-0.5852-0.8401-0.38540.21780.83630.625102.7881-0.3452-0.01832.8280.07882.413373.5545-6.22684.5283
7-0.1465-0.12530.1057-0.20740.01780.02491.28490.14170.50770.79531.68622.4158-0.31550.4293-01.69430.00360.36841.79690.18882.291270.73714.26290.1771
80.0727-0.0377-0.2155-0.1512-0.0560.19430.1396-0.29770.8549-0.29261.6363-0.55430.13113.2704-02.3424-0.69390.39751.9376-0.56842.468774.4174-0.111950.0928
90.4357-0.9480.22310.7727-0.04840.17121.75410.93830.5418-1.5669-0.71321.04560.80272.6221-01.56660.17930.70650.8975-0.12322.144563.55842.688534.8697
100.0052-0.2707-0.02540.66350.11290.05811.1970.029-1.2469-0.0720.5531-1.1709-2.3177-2.046802.0124-0.33190.00112.58030.23042.555865.1787-4.6189-3.3832
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 16:100)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 101:199)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 200:309)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 310:394)
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 401:445)
6X-RAY DIFFRACTION6CHAIN A AND (RESSEQ 446:475)
7X-RAY DIFFRACTION7CHAIN A AND (RESSEQ 528:551)
8X-RAY DIFFRACTION8CHAIN A AND (RESSEQ 559:585)
9X-RAY DIFFRACTION9CHAIN A AND (RESSEQ 586:610)
10X-RAY DIFFRACTION10CHAIN A AND (RESSEQ 611:637)

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