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- PDB-7agb: Protease Sapp1p from Candida parapsilosis in complex with KB70 -

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Basic information

Entry
Database: PDB / ID: 7agb
TitleProtease Sapp1p from Candida parapsilosis in complex with KB70
Components
  • Candidapepsin
  • KB70
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
Chem-PE3 / TRIETHYLENE GLYCOL / candidapepsin
Similarity search - Component
Biological speciesCandida parapsilosis (yeast)
Streptomyces albus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.7 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: KB70
J: KB70
K: KB70
L: KB70
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,89734
Polymers146,8258
Non-polymers4,07326
Water13,583754
1
A: Candidapepsin
I: KB70
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8089
Polymers36,7062
Non-polymers1,1027
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Candidapepsin
J: KB70
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8597
Polymers36,7062
Non-polymers1,1535
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Candidapepsin
K: KB70
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5708
Polymers36,7062
Non-polymers8646
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Candidapepsin
L: KB70
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,65910
Polymers36,7062
Non-polymers9538
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)172.021, 172.021, 252.692
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
KB70


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

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Non-polymers , 6 types, 780 molecules

#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C6H14O4
#5: 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
#6: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#7: Chemical ChemComp-PE3 / 3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL / POLYETHYLENE GLYCOL / Polyethylene glycol


Mass: 634.751 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H58O15
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 754 / 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

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: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 26, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 234657 / % possible obs: 98.3 % / Redundancy: 14.5 % / Biso Wilson estimate: 31.1 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.094 / Rrim(I) all: 0.098 / Net I/σ(I): 19.7
Reflection shellResolution: 1.7→1.75 Å / Redundancy: 13.5 % / Rmerge(I) obs: 1.61 / Mean I/σ(I) obs: 1.85 / Num. unique obs: 15854 / CC1/2: 0.69 / Rrim(I) all: 1.67 / % possible all: 90.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3FV3

3fv3


Resolution: 1.7→34.58 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.957 / SU B: 3.448 / SU ML: 0.059 / SU R Cruickshank DPI: 0.0796 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.08 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1972 11694 5 %RANDOM
Rwork0.1788 ---
obs0.1797 221558 97.49 %-
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: 118.08 Å2 / Biso mean: 34.746 Å2 / Biso min: 15.06 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å2-0.09 Å2-0 Å2
2---0.18 Å20 Å2
3---0.58 Å2
Refinement stepCycle: final / Resolution: 1.7→34.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10289 0 228 757 11274
Biso mean--50.33 38.04 -
Num. residues----1384
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0210891
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210002
X-RAY DIFFRACTIONr_angle_refined_deg1.6691.96814827
X-RAY DIFFRACTIONr_angle_other_deg0.9993.00222952
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.85651441
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.00726.045440
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.383151620
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.5731521
X-RAY DIFFRACTIONr_chiral_restr0.0940.21726
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212601
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022392
LS refinement shellResolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 759 -
Rwork0.275 14326 -
all-15085 -
obs--86.45 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.271-0.07270.04240.1206-0.11810.31070.07170.02220.0263-0.0161-0.0636-0.04440.0755-0.1004-0.00810.1258-0.0345-0.00120.34640.02520.0438-33.64956.81284.555
20.1860.1193-0.02360.16960.11210.21610.0115-0-0.00150.014-0.00070.01590.01380.0341-0.01080.1465-0.06060.0140.29890.02610.0531-32.98457.235139.127
30.3216-0.0039-0.10910.1179-0.30691.08-0.02640.0396-0.0153-0.05990.12910.0210.1503-0.2781-0.10270.2151-0.1959-0.02790.3220.07540.0638-58.27432.813126.652
40.1589-0.0609-0.14980.11940.06830.55860.09410.01240.0090.00860.0004-0.0024-0.0330.038-0.09450.1270.02680.03910.30840.00340.0612-0.28266.8496.945
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 339
2X-RAY DIFFRACTION2B1 - 339
3X-RAY DIFFRACTION3C1 - 339
4X-RAY DIFFRACTION4D1 - 339

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