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- PDB-1j71: Structure of the extracellular aspartic proteinase from Candida t... -

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Basic information

Entry
Database: PDB / ID: 1j71
TitleStructure of the extracellular aspartic proteinase from Candida tropicalis yeast.
Components
  • Aspartic proteinase
  • Tetrapeptide Thr-Ile-Thr-Ser
KeywordsHYDROLASE / Candida tropicalis aspartic protease / SAPT1
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. / 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
ETHANOL / Candidapepsin
Similarity search - Component
Biological speciesCandida tropicalis (yeast)
unidentified (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSymersky, J. / Monod, M. / Foundling, S.I.
CitationJournal: Biochemistry / Year: 1997
Title: High-resolution structure of the extracellular aspartic proteinase from Candida tropicalis yeast.
Authors: Symersky, J. / Monod, M. / Foundling, S.I.
History
DepositionMay 15, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Aug 16, 2023Group: Data collection / Database references ...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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aspartic proteinase
B: Tetrapeptide Thr-Ile-Thr-Ser
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6518
Polymers36,3752
Non-polymers2766
Water4,161231
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.960, 51.430, 128.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Aspartic proteinase / candidapepsin


Mass: 35954.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida tropicalis (yeast) / References: UniProt: Q00663, candidapepsin
#2: Protein/peptide Tetrapeptide Thr-Ile-Thr-Ser


Mass: 420.458 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) unidentified (others)
#3: Chemical
ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: VAPOR DIFFUSION BY HANGING DROPS. 0.1 M SODIUM ACETATE, 20% ETHANOL, 1:1 WITH WATER SOLUTION OF THE PROTEIN (30 MG/ML)., pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
130 mg/mlprotein1drop
20.1 Msodium acetate1reservoir
320 %ethanol1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418 Å
DetectorType: SIEMENS-NICOLET X100 / Detector: AREA DETECTOR / Date: Jun 27, 1994 / Details: monochromator
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. all: 110551 / Num. obs: 99496 / % possible obs: 93 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1.36 / Redundancy: 3.5 % / Biso Wilson estimate: 14.7 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 19
Reflection
*PLUS
Num. obs: 32636 / Num. measured all: 215435 / Rmerge(I) obs: 0.068

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Processing

Software
NameVersionClassification
FRAMBOdata collection
SAINTdata reduction
AMoREphasing
CNS1refinement
SAINTdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1ZAP

1zap


Resolution: 1.8→27.52 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 60546.12 / Data cutoff high rms absF: 10000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: A POSTERIORI / σ(F): 2 / σ(I): 1.36 / Stereochemistry target values: Engh & Huber
Details: A TETRAPEPTIDE OF UNKNOWN SOURCE FOUND AT THE ACTIVE SITE REFINED BEST AS THR-ILE-THR-SER. HOWEVER, THR COULD ALSO BE A VAL. IN ADDITION, FIVE AMINO ACID RESIDUES IN THE ENZYME SEQUENCE HAVE ...Details: A TETRAPEPTIDE OF UNKNOWN SOURCE FOUND AT THE ACTIVE SITE REFINED BEST AS THR-ILE-THR-SER. HOWEVER, THR COULD ALSO BE A VAL. IN ADDITION, FIVE AMINO ACID RESIDUES IN THE ENZYME SEQUENCE HAVE BEEN REASSIGNED BASED ON THE ELECTRON DENSITY AT 1.8 A RESOLUTION; SEE SEQADV.
RfactorNum. reflection% reflectionSelection details
Rfree0.193 1441 4.9 %RANDOM
Rwork0.1647 ---
all0.171 29883 --
obs0.1675 29319 92.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.52 Å2 / ksol: 0.303 e/Å3
Displacement parametersBiso mean: 19.9 Å2
Baniso -1Baniso -2Baniso -3
1-2.66 Å20 Å20 Å2
2---1.09 Å20 Å2
3----1.57 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.17 Å
Luzzati d res low-30 Å
Luzzati sigma a0.1 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 1.8→27.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2560 0 0 249 2809
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d26.2
X-RAY DIFFRACTIONc_improper_angle_d0.72
X-RAY DIFFRACTIONc_mcbond_it1.271.5
X-RAY DIFFRACTIONc_mcangle_it2.052
X-RAY DIFFRACTIONc_scbond_it2.112
X-RAY DIFFRACTIONc_scangle_it3.112.5
LS refinement shellResolution: 1.8→1.85 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.218 122 5.9 %
Rwork0.188 1949 -
obs-1949 80.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMPROTEIN.LINK
X-RAY DIFFRACTION3ETH.PARAMWATER.TOP
X-RAY DIFFRACTION4ETH.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 8 Å / Num. reflection obs: 28918 / σ(F): 2 / % reflection Rfree: 4.9 % / Rfactor obs: 0.183 / Rfactor Rfree: 0.226
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 16.6 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg0.764
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.72
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.218 / % reflection Rfree: 5.9 % / Rfactor Rwork: 0.188

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