[English] 日本語
Yorodumi
- PDB-3rzf: Crystal Structure of Inhibitor of kappaB kinase beta (I4122) -

+
Open data


ID or keywords:

Loading...

-
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 ...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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MGC80376 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,4392
Polymers78,0021
Non-polymers4381
Water00
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more