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- PDB-2qzx: Secreted aspartic proteinase (Sap) 5 from Candida albicans -

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Basic information

Entry
Database: PDB / ID: 2qzx
TitleSecreted aspartic proteinase (Sap) 5 from Candida albicans
Components
  • Candidapepsin-5
  • Pepstatin
KeywordsHYDROLASE/HYDROLASE INHIBITOR / aspartic proteinase / Candida albicans / Aspartyl protease / Cleavage on pair of basic residues / Glycoprotein / Protease / Secreted / Zymogen / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


candidapepsin / fungal biofilm matrix / fungal-type cell wall organization / fungal-type cell wall / single-species biofilm formation / : / 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. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily ...Secreted aspartic endopeptidase / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Pepstatin / Candidapepsin-5
Similarity search - Component
Biological speciesCandida albicans (yeast)
Streptomyces argenteolus subsp. toyonakensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsLee, J.H. / Ruge, E. / Borelli, C. / Maskos, K. / Huber, R.
CitationJournal: Proteins / Year: 2008
Title: X-ray structures of Sap1 and Sap5: Structural comparison of the secreted aspartic proteinases from Candida albicans.
Authors: Borelli, C. / Ruge, E. / Lee, J.H. / Schaller, M. / Vogelsang, A. / Monod, M. / Korting, H.C. / Huber, R. / Maskos, K.
History
DepositionAug 17, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.2Feb 27, 2013Group: Other
Revision 1.3Oct 25, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_residues / software
Revision 1.4Aug 30, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / 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_residues / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Candidapepsin-5
B: Candidapepsin-5
C: Pepstatin
D: Pepstatin


Theoretical massNumber of molelcules
Total (without water)75,8494
Polymers75,8494
Non-polymers00
Water6,666370
1
A: Candidapepsin-5
C: Pepstatin


Theoretical massNumber of molelcules
Total (without water)37,9252
Polymers37,9252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint-11 kcal/mol
Surface area14990 Å2
MethodPISA
2
B: Candidapepsin-5
D: Pepstatin


Theoretical massNumber of molelcules
Total (without water)37,9252
Polymers37,9252
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint-9 kcal/mol
Surface area15050 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4410 Å2
ΔGint-29 kcal/mol
Surface area28310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.196, 92.196, 182.005
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-2179-

HOH

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Components

#1: Protein Candidapepsin-5 / Aspartate protease 5 / ACP 5 / Secreted aspartic protease 5


Mass: 37238.738 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans (yeast) / Production host: Pichia pastoris (fungus) / References: UniProt: P43094, candidapepsin
#2: Protein/peptide Pepstatin


Type: Oligopeptide / Class: Enzyme inhibitor / Mass: 685.891 Da / Num. of mol.: 2 / Source method: obtained synthetically
Source: (synth.) Streptomyces argenteolus subsp. toyonakensis (bacteria)
References: Pepstatin
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 370 / 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: 2.6 Å3/Da / Density % sol: 52.63 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 10% PEG 8000, 8% Ethylene Glycol, 0.1 M HEPES/NaOH, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 10, 2005
RadiationMonochromator: Si(III) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. all: 27869 / Num. obs: 26813 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.108 / Χ2: 1.099 / Net I/σ(I): 7.1
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.458 / Num. unique all: 2716 / Χ2: 0.971 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT2data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1ZAP

1zap


Resolution: 2.5→30 Å / Cross valid method: THROUGHOUT / σ(F): 1476 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.275 1263 4.5 %RANDOM
Rwork0.224 ---
all0.246 27930 --
obs-26393 94.5 %-
Solvent computationBsol: 13.751 Å2
Displacement parametersBiso mean: 26.696 Å2
Baniso -1Baniso -2Baniso -3
1--3.477 Å20 Å20 Å2
2---3.477 Å20 Å2
3---6.955 Å2
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5342 0 0 370 5712
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.377
X-RAY DIFFRACTIONc_mcbond_it2.0682
X-RAY DIFFRACTIONc_scbond_it4.8784
X-RAY DIFFRACTIONc_mcangle_it3.263
X-RAY DIFFRACTIONc_scangle_it6.2655
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.protein.top
X-RAY DIFFRACTION2water_rep.pawater.top
X-RAY DIFFRACTION3DRGCNS-mf-inh-mov.PARDRGCNS-mf-inh-mov.TOP

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