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- PDB-4uuc: Crystal structure of human ASB11 ankyrin repeat domain -

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Basic information

Entry
Database: PDB / ID: 4uuc
TitleCrystal structure of human ASB11 ankyrin repeat domain
ComponentsANKYRIN REPEAT AND SOCS BOX PROTEIN 11
KeywordsSIGNALING PROTEIN
Function / homology
Function and homology information


protein K11-linked ubiquitination / Cul5-RING ubiquitin ligase complex / ubiquitin-like ligase-substrate adaptor activity / endoplasmic reticulum unfolded protein response / positive regulation of protein catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / Neddylation / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / endoplasmic reticulum / cytosol
Similarity search - Function
Ankyrin repeat and SOCS box protein 9/11, SOCS box domain / : / SOCS box / SOCS box-like domain superfamily / SOCS box domain / SOCS box domain profile. / SOCS_box / Ankyrin repeats (many copies) / Ankyrin repeat-containing domain / Ankyrin repeats (3 copies) ...Ankyrin repeat and SOCS box protein 9/11, SOCS box domain / : / SOCS box / SOCS box-like domain superfamily / SOCS box domain / SOCS box domain profile. / SOCS_box / Ankyrin repeats (many copies) / Ankyrin repeat-containing domain / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Ankyrin repeat-containing domain superfamily / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
Ankyrin repeat and SOCS box protein 11
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPinkas, D.M. / Sanvitale, C. / Kragh Nielsen, T. / Guo, K. / Sorrell, F. / Berridge, G. / Ayinampudi, V. / Wang, D. / Newman, J.A. / Tallant, C. ...Pinkas, D.M. / Sanvitale, C. / Kragh Nielsen, T. / Guo, K. / Sorrell, F. / Berridge, G. / Ayinampudi, V. / Wang, D. / Newman, J.A. / Tallant, C. / Chaikuad, A. / Canning, P. / Kopec, J. / Krojer, T. / Vollmar, M. / Allerston, C.K. / Chalk, R. / Burgess-Brown, N. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Bullock, A.
CitationJournal: To be Published
Title: Crystal Structure of Human Asb11 Ankyrin Repeat Domain
Authors: Pinkas, D.M. / Sanvitale, C. / Kragh Nielsen, T. / Guo, K. / Sorrell, F. / Berridge, G. / Ayinampudi, V. / Wang, D. / Newman, J.A. / Tallant, C. / Chaikuad, A. / Canning, P. / Kopec, J. / ...Authors: Pinkas, D.M. / Sanvitale, C. / Kragh Nielsen, T. / Guo, K. / Sorrell, F. / Berridge, G. / Ayinampudi, V. / Wang, D. / Newman, J.A. / Tallant, C. / Chaikuad, A. / Canning, P. / Kopec, J. / Krojer, T. / Vollmar, M. / Allerston, C.K. / Chalk, R. / Burgess-Brown, N. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Bullock, A.
History
DepositionJul 25, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 6, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 13, 2014Group: Atomic model
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ANKYRIN REPEAT AND SOCS BOX PROTEIN 11


Theoretical massNumber of molelcules
Total (without water)23,9991
Polymers23,9991
Non-polymers00
Water4,378243
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.215, 64.375, 89.603
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ANKYRIN REPEAT AND SOCS BOX PROTEIN 11 / ASB-11 / ANKYRIN REPEAT AND SOCS BOX CONTAINING 11


Mass: 23998.590 Da / Num. of mol.: 1 / Fragment: ANKYRIN REPEAT DOMAIN, RESIDUES 64-287
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q8WXH4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / 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: 2.6 Å3/Da / Density % sol: 52.72 % / Description: NONE
Crystal growpH: 5.5
Details: 0.2M AMMONIUM ACETATE, 25% PEG3350, 0.1M BIS-TRIS PH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.8→89.6 Å / Num. obs: 23795 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Biso Wilson estimate: 22.8 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.1
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 3 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 2.3 / % possible all: 98.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZKJ

3zkj


Resolution: 1.8→52.281 Å / SU ML: 0.19 / σ(F): 1.35 / Phase error: 18.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2023 1135 4.8 %
Rwork0.1617 --
obs0.1635 23735 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.86 Å2
Refinement stepCycle: LAST / Resolution: 1.8→52.281 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1635 0 0 243 1878
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041675
X-RAY DIFFRACTIONf_angle_d0.7522283
X-RAY DIFFRACTIONf_dihedral_angle_d12.926605
X-RAY DIFFRACTIONf_chiral_restr0.028274
X-RAY DIFFRACTIONf_plane_restr0.004300
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.88190.2771410.23382791X-RAY DIFFRACTION100
1.8819-1.98120.24511360.20412771X-RAY DIFFRACTION100
1.9812-2.10530.24871470.18412761X-RAY DIFFRACTION100
2.1053-2.26780.21941590.1662797X-RAY DIFFRACTION99
2.2678-2.49610.19591270.14792817X-RAY DIFFRACTION100
2.4961-2.85720.16631310.14522832X-RAY DIFFRACTION100
2.8572-3.59970.20461460.1522870X-RAY DIFFRACTION100
3.5997-52.3030.18341480.15832961X-RAY DIFFRACTION99

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