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- PDB-6r6a: Major aspartyl peptidase 1 from C. neoformans -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 6r6a
TitleMajor aspartyl peptidase 1 from C. neoformans
Components
  • Endopeptidase
  • Pepstatin
KeywordsHYDROLASE / aspartyl protease / secreted / Cryptococcus neoformans
Function / homology
Function and homology information


aspartic-type endopeptidase activity / proteolysis
Similarity search - Function
Pepsin-like domain / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Aspartic peptidase domain superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Endopeptidase
Similarity search - Component
Biological speciesCryptococcus neoformans var. grubii (fungus)
Actinomyces (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.8 Å
AuthorsKrystufek, R. / Sacha, P. / Brynda, J. / Konvalinka, J.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
Ministry of Education (Czech Republic)InterBioMed LO1302 Czech Republic
CitationJournal: J.Med.Chem. / Year: 2021
Title: Re-emerging Aspartic Protease Targets: Examining Cryptococcus neoformans Major Aspartyl Peptidase 1 as a Target for Antifungal Drug Discovery.
Authors: Krystufek, R. / Sacha, P. / Starkova, J. / Brynda, J. / Hradilek, M. / Tloust'ova, E. / Grzymska, J. / Rut, W. / Boucher, M.J. / Drag, M. / Majer, P. / Hajek, M. / Rezacova, P. / Madhani, H. ...Authors: Krystufek, R. / Sacha, P. / Starkova, J. / Brynda, J. / Hradilek, M. / Tloust'ova, E. / Grzymska, J. / Rut, W. / Boucher, M.J. / Drag, M. / Majer, P. / Hajek, M. / Rezacova, P. / Madhani, H.D. / Craik, C.S. / Konvalinka, J.
History
DepositionMar 26, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 9, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 24, 2024Group: 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
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endopeptidase
D: Pepstatin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,44816
Polymers37,4792
Non-polymers1,96914
Water3,657203
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4370 Å2
ΔGint-57 kcal/mol
Surface area14650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.360, 112.641, 91.031
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-563-

HOH

21A-693-

HOH

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Components

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Protein / Protein/peptide / Sugars , 3 types, 3 molecules AD

#1: Protein Endopeptidase


Mass: 36793.285 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptococcus neoformans var. grubii (fungus)
Gene: CNAG_05872 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: J9VS02
#2: Protein/peptide Pepstatin


Mass: 685.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Actinomyces (bacteria)
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE

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Non-polymers , 6 types, 216 molecules

#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 3.33 Å3/Da / Density % sol: 63.06 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: protein (83 mg/mL) in 50 mM sodium acetate, pH 5.0, 100 mM sodium chloride with reservoir solution composed of 200 mM lithium sulfate, 45% (v/v) PEG-400, 100 mM sodium acetate pH 4.5.
PH range: 4.5 - 5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 1.54187 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Apr 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 1.8→73.66 Å / Num. obs: 39317 / % possible obs: 84.3 % / Redundancy: 3.529 % / Biso Wilson estimate: 24.365 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.087 / Rrim(I) all: 0.101 / Χ2: 1.016 / Net I/σ(I): 11.68 / Num. measured all: 138736
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.8-1.911.2520.5650.9922290.590.77129.8
1.91-2.042.0540.4042.0253200.7640.51276.1
2.04-2.23.2710.2624.3362860.9190.3195.9
2.2-2.414.0760.1986.7460210.9640.22899.8
2.41-2.74.3340.1549.1954720.9810.17699.9
2.7-3.114.3050.09514.1748520.9930.10899.6
3.11-3.814.0830.0524.2141010.9980.05799.3
3.81-5.373.3980.03430.8631820.9980.04198
5.37-73.664.1850.03533.4618540.9990.0498.3

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6R61

6r61


Resolution: 1.8→73.66 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.965 / SU ML: 0.084 / SU R Cruickshank DPI: 0.1175 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.117 / ESU R Free: 0.113
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.207 1710 4.3 %RANDOM
Rwork0.1772 ---
obs0.1785 37608 84.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 82.38 Å2 / Biso mean: 24.601 Å2 / Biso min: 9.64 Å2
Baniso -1Baniso -2Baniso -3
1--0.75 Å2-0 Å2-0 Å2
2--0.98 Å2-0 Å2
3----0.24 Å2
Refinement stepCycle: final / Resolution: 1.8→73.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2594 0 179 210 2983
Biso mean--44.96 31.72 -
Num. residues----345
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.022854
X-RAY DIFFRACTIONr_bond_other_d0.0040.022560
X-RAY DIFFRACTIONr_angle_refined_deg1.5971.9863878
X-RAY DIFFRACTIONr_angle_other_deg1.0135940
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1435377
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.34125.192104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.31715408
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.038156
X-RAY DIFFRACTIONr_chiral_restr0.0870.2454
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023186
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02613
LS refinement shellResolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.429 30 -
Rwork0.445 565 -
all-595 -
obs--17.48 %

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