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- PDB-6r61: Major aspartyl peptidase 1 from C. neoformans in complex with Inh... -

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Basic information

Entry
Database: PDB / ID: 6r61
TitleMajor aspartyl peptidase 1 from C. neoformans in complex with Inhibitor LP258
ComponentsEndopeptidase
KeywordsHYDROLASE / aspartyl protease / secreted / Cryptococcus neoformans / inhibitor complex
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
Chem-JT8 / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Endopeptidase
Similarity search - Component
Biological speciesCryptococcus neoformans (fungus)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.81 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: To Be Published
Title: Major aspartyl peptidase 1 from C. neoformans in complex with Inhibitor LP258
Authors: Krystufek, R. / Sacha, P. / Brynda, J. / Konvalinka, J.
History
DepositionMar 26, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 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

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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)38,83013
Polymers36,8111
Non-polymers2,01912
Water3,441191
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint2 kcal/mol
Surface area14510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.170, 113.390, 91.220
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-529-

HOH

21A-670-

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 (fungus) / Gene: CNAG_05872 / Plasmid: pMT_BIP_MayI(17-434)Avitag / Production host: Drosophila melanogaster (fruit fly) / Variant (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 , 7 types, 202 molecules

#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Chemical ChemComp-JT8 / (3~{S},7~{S},8~{S})-7-oxidanyl-8-(phenylmethyl)-3-(pyridin-2-ylmethyl)-1,4,9-triazacyclotricosane-2,5,10-trione


Mass: 564.759 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H48N4O4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / 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: 3.41 Å3/Da / Density % sol: 63.96 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: peptidase (85 mg/ml) in 50 mM sodium acetate, pH=5.0, 100mM NaCl in equal volume with reservoir solution: 100mM lithium sulphate, 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 MICROMAX-007 HF / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Sep 11, 2018
RadiationMonochromator: Confocal Max-Flux optics Rigaku / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.81→73.78 Å / Num. obs: 44101 / % possible obs: 95.8 % / Redundancy: 3.764 % / Biso Wilson estimate: 24.145 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.175 / Rrim(I) all: 0.202 / Χ2: 0.892 / Net I/σ(I): 6.66
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.81-1.863.651.5250.8828490.3571.76984.5
1.86-1.913.7851.1351.2229910.5441.31291.1
1.91-1.973.8710.9031.6229860.6011.04193
1.97-2.033.8920.6292.3229750.7610.72395.7
2.03-2.093.9590.4952.9728760.8090.56897.4
2.09-2.173.980.3923.6928490.8840.44997.2
2.17-2.253.9810.3474.1927430.9060.39897.7
2.25-2.343.9630.3054.5926570.9170.3597.4
2.34-2.443.950.2715.125330.9370.31297.8
2.44-2.563.8960.2375.5324670.9590.27398
2.56-2.73.8160.2096.1523310.9610.24298.5
2.7-2.873.7260.177.1922410.9690.19799.2
2.87-3.063.5890.1279.1220910.9820.14999.6
3.06-3.313.3210.09711.2919610.9880.11599.4
3.31-3.622.7560.06813.4417850.9910.08497.1
3.62-4.052.9480.05616.5814880.9950.06788.9
4.05-4.683.8330.0520.7914580.9970.05899.7
4.68-5.734.0830.05519.7612580.9970.06499.5
5.73-8.114.0010.06517.319920.9970.07599.6
8.11-73.783.6470.0424.425700.9980.04797.8

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6R5H

6r5h


Resolution: 1.81→73.78 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.849 / SU ML: 0.081 / SU R Cruickshank DPI: 0.1073 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.107 / ESU R Free: 0.099
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2023 2240 5 %RANDOM
Rwork0.1855 ---
obs0.1864 42553 96.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 115.89 Å2 / Biso mean: 26.587 Å2 / Biso min: 8.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0 Å20 Å2
2--0.02 Å20 Å2
3----0.04 Å2
Refinement stepCycle: final / Resolution: 1.81→73.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2582 0 134 192 2908
Biso mean--45.94 33.05 -
Num. residues----350
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.022838
X-RAY DIFFRACTIONr_bond_other_d0.0030.022535
X-RAY DIFFRACTIONr_angle_refined_deg1.5181.9753854
X-RAY DIFFRACTIONr_angle_other_deg0.95235886
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8445374
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.9324.953107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.50115408
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.347157
X-RAY DIFFRACTIONr_chiral_restr0.0850.2434
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023230
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02641
LS refinement shellResolution: 1.81→1.857 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.417 145 -
Rwork0.419 2726 -
all-2871 -
obs--85.19 %

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