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- PDB-6r5h: Major aspartyl peptidase 1 from C. neoformans -

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Open data


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Basic information

Entry
Database: PDB / ID: 6r5h
TitleMajor aspartyl peptidase 1 from C. neoformans
ComponentsEndopeptidase
KeywordsHYDROLASE / aspartyl protease / secreted / Cryptococcus neoformans
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / aspartic-type endopeptidase activity / proteolysis / extracellular region
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
ACETIC ACID / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Major aspartyl peptidase 1
Similarity search - Component
Biological speciesCryptococcus neoformans var. grubii serotype A (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.75 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 25, 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 1.2Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: Endopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,11420
Polymers36,8111
Non-polymers2,30219
Water3,477193
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4420 Å2
ΔGint-20 kcal/mol
Surface area14790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.422, 112.058, 91.212
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-532-

HOH

21A-682-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Endopeptidase


Mass: 36811.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: MayI(17-434)-Avitag
Source: (gene. exp.) Cryptococcus neoformans var. grubii serotype A (strain H99 / ATCC 208821 / CBS 10515 / FGSC 9487) (fungus)
Strain: H99 / ATCC 208821 / CBS 10515 / FGSC 9487 / Gene: CNAG_05872 / Variant: var. grubii H99 / Plasmid: pMT_BiP_MayI(17-434)CAvi / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): Schneider S2 / References: UniProt: J9VS02
#2: 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 , 9 types, 211 molecules

#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


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


Mass: 106.120 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#8: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#9: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#10: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 3.38 Å3/Da / Density % sol: 63.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: MayI(17-434)-Avi (83 mg/mL) in 50 mM sodium acetate, pH 5.0, 100 mM sodium chloride in equal volume with reservoir solution 200 mM lithium sulfate, 45% (v/v) PEG-400, 100 mM NaOAc 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: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.75→48.71 Å / Num. obs: 48515 / % possible obs: 95.8 % / Redundancy: 5.45 % / Biso Wilson estimate: 29.171 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.134 / Rrim(I) all: 0.148 / Χ2: 1.062 / Net I/σ(I): 10.25 / Num. measured all: 264390
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.75-1.863.6771.2040.9763390.3961.39778.2
1.86-1.984.9090.8751.8973590.730.9896.7
1.98-2.145.9840.5623.8370770.9030.61699.8
2.14-2.355.7660.3715.9165250.9460.40899.6
2.35-2.626.0920.2428.7859420.9790.26599.9
2.62-3.035.8960.14713.2152550.9910.16199.8
3.03-3.75.8010.07722.8444890.9960.08599.8
3.7-5.225.8560.04933.4434950.9980.05399.8
5.22-48.715.5510.04434.6720340.9980.04999.1

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT3.24data extraction
MOLREPphasing
RefinementResolution: 1.75→48.71 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.944 / SU B: 3.025 / SU ML: 0.087 / SU R Cruickshank DPI: 0.0955 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.095 / ESU R Free: 0.096
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.21 2101 4.3 %RANDOM
Rwork0.1802 ---
obs0.1814 46413 95.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 93.42 Å2 / Biso mean: 29.596 Å2 / Biso min: 15.55 Å2
Baniso -1Baniso -2Baniso -3
1--1.2 Å2-0 Å20 Å2
2--1.13 Å20 Å2
3---0.07 Å2
Refinement stepCycle: final / Resolution: 1.75→48.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2578 0 146 198 2922
Biso mean--55.5 35.9 -
Num. residues----350
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.022843
X-RAY DIFFRACTIONr_bond_other_d0.0040.022545
X-RAY DIFFRACTIONr_angle_refined_deg1.5841.9763858
X-RAY DIFFRACTIONr_angle_other_deg0.98435907
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.775379
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.24925106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.80515408
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.582157
X-RAY DIFFRACTIONr_chiral_restr0.0870.2440
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023204
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02621
LS refinement shellResolution: 1.749→1.795 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.393 118 -
Rwork0.395 2589 -
all-2707 -
obs--73.02 %

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