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- PDB-5ys4: Crystal structure of retroviral protease-like domain of Ddi1 from... -

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Basic information

Entry
Database: PDB / ID: 5ys4
TitleCrystal structure of retroviral protease-like domain of Ddi1 from Leishmania major
ComponentsDNA-damage inducible protein DDI1-like protein
KeywordsHYDROLASE / retropepsin / aspartic protease / cytoplasmic
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / aspartic-type endopeptidase activity / proteolysis / cytoplasm
Similarity search - Function
Aspartic peptidase, DDI1-type / Aspartyl protease / UBA-like domain / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
DNA-damage inducible protein DDI1-like protein / Protein DDI1 homolog
Similarity search - Component
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSuguna, K. / Kumar, S.
Funding support India, 1items
OrganizationGrant numberCountry
Other governmentBT/PR1770/BRB/10/1505/2016 India
CitationJournal: FEBS Open Bio / Year: 2018
Title: Crystal structure of the retroviral protease-like domain of a protozoal DNA damage-inducible 1 protein.
Authors: Kumar, S. / Suguna, K.
History
DepositionNov 13, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 21, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: DNA-damage inducible protein DDI1-like protein
B: DNA-damage inducible protein DDI1-like protein
C: DNA-damage inducible protein DDI1-like protein
D: DNA-damage inducible protein DDI1-like protein
E: DNA-damage inducible protein DDI1-like protein
F: DNA-damage inducible protein DDI1-like protein


Theoretical massNumber of molelcules
Total (without water)87,5666
Polymers87,5666
Non-polymers00
Water6,864381
1
A: DNA-damage inducible protein DDI1-like protein
D: DNA-damage inducible protein DDI1-like protein


Theoretical massNumber of molelcules
Total (without water)29,1892
Polymers29,1892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2170 Å2
ΔGint-16 kcal/mol
Surface area11490 Å2
MethodPISA
2
B: DNA-damage inducible protein DDI1-like protein
C: DNA-damage inducible protein DDI1-like protein


Theoretical massNumber of molelcules
Total (without water)29,1892
Polymers29,1892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2270 Å2
ΔGint-16 kcal/mol
Surface area11660 Å2
MethodPISA
3
E: DNA-damage inducible protein DDI1-like protein
F: DNA-damage inducible protein DDI1-like protein


Theoretical massNumber of molelcules
Total (without water)29,1892
Polymers29,1892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2040 Å2
ΔGint-15 kcal/mol
Surface area10800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.790, 56.780, 91.400
Angle α, β, γ (deg.)76.56, 84.48, 89.99
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
DNA-damage inducible protein DDI1-like protein


Mass: 14594.268 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania major (eukaryote) / Strain: Friedlin / Gene: LMJF_01_0610 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: E9AC52, UniProt: I7HUG0*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 381 / 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: 2.7 Å3/Da / Density % sol: 53.9 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 4.5
Details: 0.1M sodium malonate, 12 % polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97625 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.3→26.34 Å / Num. obs: 36968 / % possible obs: 97.6 % / Redundancy: 2.7 % / Biso Wilson estimate: 23.6 Å2 / CC1/2: 0.985 / Rmerge(I) obs: 0.145 / Net I/σ(I): 4.9
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 3613 / CC1/2: 0.707 / % possible all: 96.8

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Processing

Software
NameVersionClassification
PHENIX1.11.1-2575refinement
PDB_EXTRACT3.1data extraction
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2I1A

2i1a


Resolution: 2.3→26.34 Å / Cross valid method: THROUGHOUT / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
RfactorNum. reflection% reflectionSelection details
Rfree0.259 1912 5.2 %RANDOM
Rwork0.236 ---
obs0.238 36967 97.6 %-
Displacement parametersBiso mean: 35.65 Å2
Baniso -1Baniso -2Baniso -3
1-1.09 Å2-0.21 Å2-0.07 Å2
2---1.87 Å20.29 Å2
3---0.8 Å2
Refinement stepCycle: LAST / Resolution: 2.3→26.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5284 0 0 381 5665
LS refinement shellResolution: 2.3→2.36 Å
RfactorNum. reflection% reflection
Rfree0.311 119 -
Rwork0.276 2548 -
obs--96.32 %

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