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- PDB-2i1a: A Retroviral Protease-Like Domain in the Eukaryotic Protein Ddi1 -

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Basic information

Entry
Database: PDB / ID: 2i1a
TitleA Retroviral Protease-Like Domain in the Eukaryotic Protein Ddi1
ComponentsDNA damage-inducible protein DDI1
KeywordsPROTEIN TURNOVER / acid protease fold / dimer / retroviral protease domain
Function / homology
Function and homology information


proteasome regulatory particle binding / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / polyubiquitin modification-dependent protein binding / protein secretion / positive regulation of DNA replication / vesicle-mediated transport / SNARE binding / ubiquitin binding / protein-macromolecule adaptor activity ...proteasome regulatory particle binding / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / polyubiquitin modification-dependent protein binding / protein secretion / positive regulation of DNA replication / vesicle-mediated transport / SNARE binding / ubiquitin binding / protein-macromolecule adaptor activity / ubiquitin-dependent protein catabolic process / aspartic-type endopeptidase activity / plasma membrane / cytoplasm
Similarity search - Function
gag-polyprotein putative aspartyl protease / DNA damage inducible protein 1 ubiquitin-like domain / Aspartic peptidase, DDI1-type / Aspartyl protease / UBA/TS-N domain / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / Peptidase A2A, retrovirus, catalytic ...gag-polyprotein putative aspartyl protease / DNA damage inducible protein 1 ubiquitin-like domain / Aspartic peptidase, DDI1-type / Aspartyl protease / UBA/TS-N domain / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / Peptidase A2A, retrovirus, catalytic / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
DNA damage-inducible protein 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MAD / Resolution: 2.3 Å
AuthorsFass, D. / Sirkis, R.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Ddi1, a eukaryotic protein with the retroviral protease fold.
Authors: Sirkis, R. / Gerst, J.E. / Fass, D.
History
DepositionAug 14, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA damage-inducible protein DDI1
B: DNA damage-inducible protein DDI1
C: DNA damage-inducible protein DDI1
D: DNA damage-inducible protein DDI1


Theoretical massNumber of molelcules
Total (without water)66,9464
Polymers66,9464
Non-polymers00
Water2,792155
1
A: DNA damage-inducible protein DDI1
B: DNA damage-inducible protein DDI1


Theoretical massNumber of molelcules
Total (without water)33,4732
Polymers33,4732
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint-16 kcal/mol
Surface area11750 Å2
MethodPISA
2
C: DNA damage-inducible protein DDI1
D: DNA damage-inducible protein DDI1


Theoretical massNumber of molelcules
Total (without water)33,4732
Polymers33,4732
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint-18 kcal/mol
Surface area11230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.800, 74.330, 153.540
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a dimer (chains A and B or chains C and D)

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Components

#1: Protein
DNA damage-inducible protein DDI1 / v-SNARE-master 1


Mass: 16736.473 Da / Num. of mol.: 4 / Fragment: retroviral protease-like domain, residues 180-325
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: DDI1, VSM1 / Plasmid: pAED4, pET3 derivative / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 plysS / References: UniProt: P40087
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 1.99 Å3/Da / Density % sol: 38.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.4
Details: 10 mM potassium phosphate, 1% dioxane, 12.5-22.5% PEG2000, pH 7.4, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418, 0.97935, 0.97949, 0.91165
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 29, 2005 / Details: osmic mirrors
RadiationMonochromator: osmic mirrors / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
20.979351
30.979491
40.911651
ReflectionResolution: 2.3→39.96 Å / Num. all: 24696 / Num. obs: 24391 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Rsym value: 0.07 / Net I/σ(I): 18.8
Reflection shellResolution: 2.3→2.38 Å / Mean I/σ(I) obs: 3.9 / Rsym value: 0.514 / % possible all: 90

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Processing

Software
NameVersionClassification
SOLVEphasing
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.3→39.96 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflectionSelection details
Rfree0.266 1654 random
Rwork0.229 --
all-24591 -
obs-24306 -
Refinement stepCycle: LAST / Resolution: 2.3→39.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3563 0 0 155 3718
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.342
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param

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