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- PDB-7age: Protease Sapp1p from Candida parapsilosis in complex with KB32 -

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Basic information

Entry
Database: PDB / ID: 7age
TitleProtease Sapp1p from Candida parapsilosis in complex with KB32
Components
  • Candidapepsin
  • Pepstatin
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
DI(HYDROXYETHYL)ETHER / candidapepsin
Similarity search - Component
Biological speciesCandida parapsilosis (yeast)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.3 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 1.1Apr 28, 2021Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Revision 1.2Jan 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
I: Pepstatin
B: Candidapepsin
C: Pepstatin
D: Candidapepsin
E: Pepstatin
F: Candidapepsin
G: Pepstatin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,09820
Polymers146,8258
Non-polymers1,27312
Water28,0131555
1
D: Candidapepsin
E: Pepstatin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3438
Polymers36,7062
Non-polymers6376
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Candidapepsin
I: Pepstatin


  • defined by author&software
  • 36.7 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)36,7062
Polymers36,7062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-3 kcal/mol
Surface area14270 Å2
MethodPISA
3
B: Candidapepsin
C: Pepstatin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0255
Polymers36,7062
Non-polymers3183
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint-3 kcal/mol
Surface area14010 Å2
MethodPISA
4
F: Candidapepsin
G: Pepstatin
hetero molecules


  • defined by author&software
  • 37 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)37,0255
Polymers36,7062
Non-polymers3183
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2190 Å2
ΔGint5 kcal/mol
Surface area13990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.260, 87.290, 157.950
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#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
Pepstatin /


Mass: 841.002 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: Chemically synthesized / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1555 / Source method: isolated from a natural source / Formula: H2O
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: 2.03 Å3/Da / Density % sol: 39.34 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
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: 0.9184 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: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.25→79.315 Å / Num. all: 323787 / Num. obs: 323787 / % possible obs: 96.6 % / Redundancy: 4.8 % / Rpim(I) all: 0.033 / Rrim(I) all: 0.073 / Rsym value: 0.06 / Net I/av σ(I): 8.5 / Net I/σ(I): 11.4 / Num. measured all: 1558037
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
1.25-1.2840.5481.475302187070.3380.7080.5482.176.5
1.28-1.324.30.4591.796926222950.2760.5920.4592.693.1
1.32-1.364.90.3752.1110694227230.2120.4760.3753.397.3
1.36-1.44.90.3152.5108130221100.1770.3980.3153.997.6
1.4-1.444.90.2543.1105503215580.1430.3220.2544.797.8
1.44-1.494.90.2113.7102201208350.1180.2660.2115.598
1.49-1.554.90.1734.598910202030.0970.2180.1736.598.3
1.55-1.614.90.145.595686194680.0780.1760.147.798.5
1.61-1.694.90.1146.792220187480.0630.1430.1149.198.6
1.69-1.774.90.0938.288464179710.0510.1160.09310.798.9
1.77-1.864.90.0741084679171700.0410.0920.07413.199
1.86-1.984.90.06111.879909162230.0330.0750.06116.199.1
1.98-2.114.90.0541375572153370.0290.0650.0541999.3
2.11-2.284.90.05213.270628143320.0270.0620.05221.199.5
2.28-2.54.90.05412.165120132310.0280.0630.0542299.6
2.5-2.84.90.0531259088120290.0270.0620.05323.899.7
2.8-3.234.90.0421552376106830.0220.050.04227.599.9
3.23-3.954.90.03319.14428290800.0180.0390.03331.499.8
3.95-5.594.80.02920.73427071140.0150.0340.02931.999.9
5.59-23.2634.60.02421.31807739700.0130.0290.02425.697.4

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.8 Å23.15 Å
Translation3.8 Å23.15 Å

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0103refinement
MOSFLMdata reduction
SCALA3.3.16data scaling
MOLREP10.2.35phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TNE

3tne


Resolution: 1.3→23.14 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.964 / WRfactor Rfree: 0.1784 / WRfactor Rwork: 0.1595 / FOM work R set: 0.8928 / SU B: 0.791 / SU ML: 0.033 / SU R Cruickshank DPI: 0.0503 / SU Rfree: 0.0508 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.05 / ESU R Free: 0.051 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1804 14594 5.1 %RANDOM
Rwork0.1617 ---
obs0.1626 274147 98.39 %-
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: 68.99 Å2 / Biso mean: 13.17 Å2 / Biso min: 4.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.04 Å2-0 Å2
3----0.06 Å2
Refinement stepCycle: final / Resolution: 1.3→23.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10307 0 84 1565 11956
Biso mean--41.57 22.28 -
Num. residues----1381
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0210950
X-RAY DIFFRACTIONr_bond_other_d0.0090.0210050
X-RAY DIFFRACTIONr_angle_refined_deg1.5891.95914944
X-RAY DIFFRACTIONr_angle_other_deg1.9243.00323084
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.17851485
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.89525.921456
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.176151681
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2291527
X-RAY DIFFRACTIONr_chiral_restr0.0930.21759
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212769
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022425
LS refinement shellResolution: 1.302→1.336 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 1050 -
Rwork0.247 19750 -
all-20800 -
obs--97.02 %

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