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- PDB-5yq8: Crystal structure of retroviral protease-like domain of Ddi1 from... -

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Basic information

Entry
Database: PDB / ID: 5yq8
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 / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsSuguna, K. / Kumar, S.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT)-Indian Institute of Science, Partnership program for advanced Research in Biological Science and Bioengineering 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 6, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 19, 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

Downloads & links

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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


Theoretical massNumber of molelcules
Total (without water)58,2414
Polymers58,2414
Non-polymers00
Water8,647480
1
A: DNA-damage inducible protein DDI1-like protein
B: DNA-damage inducible protein DDI1-like protein


Theoretical massNumber of molelcules
Total (without water)29,1212
Polymers29,1212
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2250 Å2
ΔGint-16 kcal/mol
Surface area12910 Å2
MethodPISA
2
C: DNA-damage inducible protein DDI1-like protein
D: DNA-damage inducible protein DDI1-like protein


Theoretical massNumber of molelcules
Total (without water)29,1212
Polymers29,1212
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2250 Å2
ΔGint-16 kcal/mol
Surface area12630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.530, 80.390, 85.450
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 14560.252 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania major (eukaryote) / 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.: 480 / 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: 2.1 Å3/Da / Density % sol: 41.4 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 4.5
Details: 0.1 M sodium acetate trihydrate, 30 % polyethylene glycol 1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.514
11-h,-k,l20.486
ReflectionResolution: 2.25→58.55 Å / Num. obs: 22170 / % possible obs: 96.76 % / Redundancy: 2.6 % / CC1/2: 0.971 / Rmerge(I) obs: 0.136 / Rpim(I) all: 0.136 / Net I/σ(I): 5.9
Reflection shellResolution: 2.25→2.32 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 2068 / CC1/2: 0.324 / Rpim(I) all: 0.339 / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2I1A

2i1a


Resolution: 2.25→42.72 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.835 / SU B: 4.305 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.054 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23981 1069 4.8 %RANDOM
Rwork0.1642 ---
obs0.16788 21101 96.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.669 Å2
Baniso -1Baniso -2Baniso -3
1-1.33 Å20 Å22.12 Å2
2---3.1 Å2-0 Å2
3---1.77 Å2
Refinement stepCycle: 1 / Resolution: 2.25→42.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3927 0 0 480 4407
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0193985
X-RAY DIFFRACTIONr_bond_other_d0.0030.023876
X-RAY DIFFRACTIONr_angle_refined_deg1.8551.9725391
X-RAY DIFFRACTIONr_angle_other_deg1.09538956
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8735506
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.14624.545165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.5515725
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1991525
X-RAY DIFFRACTIONr_chiral_restr0.0980.2644
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214365
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02736
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4861.742035
X-RAY DIFFRACTIONr_mcbond_other1.4791.7392034
X-RAY DIFFRACTIONr_mcangle_it2.3412.6032536
X-RAY DIFFRACTIONr_mcangle_other2.342.6052537
X-RAY DIFFRACTIONr_scbond_it1.2151.7031950
X-RAY DIFFRACTIONr_scbond_other1.2151.7051951
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.8832.5362856
X-RAY DIFFRACTIONr_long_range_B_refined4.96730.77716239
X-RAY DIFFRACTIONr_long_range_B_other4.77130.88115840
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 101 -
Rwork0.195 1559 -
obs--98.75 %

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