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- PDB-1i2t: X-RAY STRUCTURE OF THE HUMAN HYPERPLASTIC DISCS PROTEIN: AN ORTHO... -

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Basic information

Entry
Database: PDB / ID: 1i2t
TitleX-RAY STRUCTURE OF THE HUMAN HYPERPLASTIC DISCS PROTEIN: AN ORTHOLOG OF THE C-TERMINAL DOMAIN OF POLY(A)-BINDING PROTEIN
ComponentsHYD PROTEIN
KeywordsLIGASE / Four alpha-helical domain
Function / homology
Function and homology information


heterochromatin boundary formation / HECT-type E3 ubiquitin transferase / DNA repair-dependent chromatin remodeling / ubiquitin-ubiquitin ligase activity / progesterone receptor signaling pathway / protein K48-linked ubiquitination / ubiquitin binding / protein polyubiquitination / positive regulation of protein import into nucleus / positive regulation of canonical Wnt signaling pathway ...heterochromatin boundary formation / HECT-type E3 ubiquitin transferase / DNA repair-dependent chromatin remodeling / ubiquitin-ubiquitin ligase activity / progesterone receptor signaling pathway / protein K48-linked ubiquitination / ubiquitin binding / protein polyubiquitination / positive regulation of protein import into nucleus / positive regulation of canonical Wnt signaling pathway / ubiquitin protein ligase activity / DNA repair / DNA damage response / positive regulation of gene expression / perinuclear region of cytoplasm / protein-containing complex / RNA binding / zinc ion binding / nucleoplasm / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
: / E3 ubiquitin ligase EDD, ubiquitin-associated domain / E3 ubiquitin ligase EDD / c-terminal domain of poly(a) binding protein / c-terminal domain of poly(a) binding protein / Polyadenylate-binding protein/Hyperplastic disc protein / Poly-adenylate binding protein, unique domain / Poly(A)-binding protein C-terminal (PABC) domain profile. / C-terminal domain of Poly(A)-binding protein. Present also in Drosophila hyperplastics discs protein. / PABC (PABP) domain ...: / E3 ubiquitin ligase EDD, ubiquitin-associated domain / E3 ubiquitin ligase EDD / c-terminal domain of poly(a) binding protein / c-terminal domain of poly(a) binding protein / Polyadenylate-binding protein/Hyperplastic disc protein / Poly-adenylate binding protein, unique domain / Poly(A)-binding protein C-terminal (PABC) domain profile. / C-terminal domain of Poly(A)-binding protein. Present also in Drosophila hyperplastics discs protein. / PABC (PABP) domain / Zinc finger, UBR-type / Zinc finger UBR-type profile. / Putative zinc finger in N-recognin, a recognition component of the N-end rule pathway / Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. / Domain Homologous to E6-AP Carboxyl Terminus with / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
E3 ubiquitin-protein ligase UBR5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.04 Å
AuthorsDeo, R.C. / Sonenberg, N. / Burley, S.K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: X-ray structure of the human hyperplastic discs protein: an ortholog of the C-terminal domain of poly(A)-binding protein.
Authors: Deo, R.C. / Sonenberg, N. / Burley, S.K.
History
DepositionFeb 12, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Structure summary / Category: audit_author / citation_author
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HYD PROTEIN


Theoretical massNumber of molelcules
Total (without water)6,7491
Polymers6,7491
Non-polymers00
Water2,342130
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.969, 38.166, 51.062
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 HYD PROTEIN


Mass: 6748.893 Da / Num. of mol.: 1 / Fragment: HYPERPLASTIC DISCS DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HYD / Plasmid: PET28A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: O95071, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 2.38 Å3/Da / Density % sol: 48.3 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Dioxane, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.25
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
114 mg/mlprotein1drop
2100 mM1dropNaCl
320 mMHEPES1drop
434 %1,4-dioxane1reservoir

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.1 Å
DetectorType: SBC-2 / Detector: CCD / Date: Jul 2, 2000 / Details: mirrors
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.04→20 Å / Num. all: 461426 / Num. obs: 460042 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13 % / Biso Wilson estimate: 7 Å2 / Rmerge(I) obs: 0.059 / Rsym value: 5.9 / Net I/σ(I): 38
Reflection shellResolution: 1.04→20 Å / Redundancy: 5 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 3 / Num. unique all: 2014 / Rsym value: 30 / % possible all: 97
Reflection
*PLUS
Num. obs: 31619 / Num. measured all: 460042
Reflection shell
*PLUS
% possible obs: 97 %

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Processing

Software
NameClassification
MLPHAREphasing
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.04→20 Å / σ(F): 4 / σ(I): 4 / Stereochemistry target values: Engh and Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.171 1575 -random
Rwork0.143 ---
all0.154 31407 --
obs0.143 25221 85 %-
Refinement stepCycle: LAST / Resolution: 1.04→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms472 0 0 130 602
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.0108
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg2.06

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