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- PDB-7agd: Protease Sapp1p from Candida parapsilosis in complex with KB75 -

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Basic information

Entry
Database: PDB / ID: 7agd
TitleProtease Sapp1p from Candida parapsilosis in complex with KB75
Components
  • Candidapepsin
  • KB75
KeywordsANTIBIOTIC / Secreted aspartic protease / virulence factor / candidiasis / peptidomimetic inhibitors
Function / homology
Function and homology information


candidapepsin / aspartic-type endopeptidase activity / proteolysis / extracellular region
Similarity search - Function
Secreted aspartic endopeptidase / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily
Similarity search - Domain/homology
FORMYL GROUP / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / candidapepsin
Similarity search - Component
Biological speciesCandida parapsilosis (yeast)
Streptomyces albus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsDostal, J. / Heidingsfeld, O. / Brynda, J.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
Ministry of Education (MoE, Czech Republic)CZ.02.1.01/0.0/16_019/000729 Czech Republic
CitationJournal: J Enzyme Inhib Med Chem / Year: 2021
Title: Structural determinants for subnanomolar inhibition of the secreted aspartic protease Sapp1p from Candida parapsilosis .
Authors: Dostal, J. / Brynda, J. / Vankova, L. / Zia, S.R. / Pichova, I. / Heidingsfeld, O. / Lepsik, M.
History
DepositionSep 22, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 21, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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: Candidapepsin
B: Candidapepsin
C: Candidapepsin
D: Candidapepsin
I: KB75
J: KB75
K: KB75
L: KB75
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,10617
Polymers146,8258
Non-polymers1,2819
Water14,016778
1
A: Candidapepsin
I: KB75
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0514
Polymers36,7062
Non-polymers3442
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint-0 kcal/mol
Surface area13810 Å2
MethodPISA
2
B: Candidapepsin
J: KB75
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0825
Polymers36,7062
Non-polymers3753
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint-2 kcal/mol
Surface area14150 Å2
MethodPISA
3
C: Candidapepsin
K: KB75
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8563
Polymers36,7062
Non-polymers1501
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-6 kcal/mol
Surface area13990 Å2
MethodPISA
4
D: Candidapepsin
L: KB75
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1185
Polymers36,7062
Non-polymers4113
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2020 Å2
ΔGint-13 kcal/mol
Surface area13880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)172.620, 172.620, 253.252
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222

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Components

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Protein / Protein/peptide , 2 types, 8 molecules ABCDIJKL

#1: Protein
Candidapepsin /


Mass: 35865.160 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida parapsilosis (yeast) / Gene: SAPP1 / Production host: Candida parapsilosis (yeast) / References: UniProt: B8YPM3, candidapepsin
#2: Protein/peptide
KB75


Mass: 841.002 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Streptomyces albus (bacteria)

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Non-polymers , 7 types, 787 molecules

#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Chemical ChemComp-FOR / FORMYL GROUP / Aldehyde


Mass: 30.026 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 778 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.68 Å3/Da / Density % sol: 66.6 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: 100-fold molar inhibitor excess, Cpr=20mg/ml; drops: 0.002ml protein + 0.001ml reservoir; reservoir: 0.1M MES pH 6.5, 30% v/v PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Dec 15, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.8→253.252 Å / Num. all: 202267 / Num. obs: 202267 / % possible obs: 99.3 % / Redundancy: 9.7 % / Rpim(I) all: 0.039 / Rrim(I) all: 0.125 / Rsym value: 0.113 / Net I/av σ(I): 4.8 / Net I/σ(I): 12.1 / Num. measured all: 1960056
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.8-1.856.40.9210.886995136670.4191.0970.9211.692.2
1.85-1.97.10.7821102900144130.3330.9160.7822.199.4
1.9-1.9590.6581.2127202141170.2440.7410.6583.1100
1.95-2.0110.30.5581.4141797137390.1910.6170.5584.1100
2.01-2.0810.40.4251.8139089133410.1450.470.4255.4100
2.08-2.1510.40.3432.3134686129020.1160.3780.3436.5100
2.15-2.2310.40.2772.8129839124440.0940.3060.2777.8100
2.23-2.3210.50.2293.4125504120050.0780.2520.2299.3100
2.32-2.4310.50.1934120827115570.0660.2130.19310.4100
2.43-2.5510.50.1614.8115465110450.0550.1780.16112.1100
2.55-2.6810.50.1335.7110169105290.0450.1460.13314100
2.68-2.8510.50.1017.310424599740.0340.1110.10116.7100
2.85-3.0410.40.0799.39783693990.0270.0860.07919.9100
3.04-3.2910.30.06410.59078587800.0220.070.06423.1100
3.29-3.610.20.0688.88317581350.0230.0730.06826100
3.6-4.02100.0786.97372573500.0260.0840.07828.1100
4.02-4.659.80.0697.56439265540.0230.0740.06930.5100
4.65-5.699.50.0479.25331155940.0170.0510.04729.9100
5.69-8.0590.03416.93981944150.0120.0370.03427.8100
8.05-18.4177.90.03113.51829523070.0120.0340.03128.490.1

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA3.3.16data scaling
REFMAC5.8.0103refinement
PDB_EXTRACT3.25data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Y9W

4y9w


Resolution: 1.8→18.42 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.944 / SU R Cruickshank DPI: 0.1019 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.102 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.223 10179 5 %RANDOM
Rwork0.2005 ---
obs0.2016 192014 99.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 135.86 Å2 / Biso mean: 29.039 Å2 / Biso min: 9.78 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å20.18 Å20 Å2
2--0.36 Å2-0 Å2
3----1.18 Å2
Refinement stepCycle: final / Resolution: 1.8→18.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10243 0 79 782 11104
Biso mean--46.55 33.46 -
Num. residues----1380
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0210693
X-RAY DIFFRACTIONr_bond_other_d00.029738
X-RAY DIFFRACTIONr_angle_refined_deg1.6281.95714601
X-RAY DIFFRACTIONr_angle_other_deg5.383.00222330
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.98851436
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.35626.212433
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.551151595
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.3951516
X-RAY DIFFRACTIONr_chiral_restr0.0940.21713
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212532
X-RAY DIFFRACTIONr_gen_planes_other0.0090.022364
LS refinement shellResolution: 1.8→1.846 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 656 -
Rwork0.31 12888 -
all-13544 -
obs--91.71 %

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