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- PDB-2jxr: STRUCTURE OF YEAST PROTEINASE A -

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Basic information

Entry
Database: PDB / ID: 2jxr
TitleSTRUCTURE OF YEAST PROTEINASE A
ComponentsPROTEINASE A
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR COMPLEX / ASPARTYL PROTEASE / GLYCOPROTEIN / ZYMOGEN
Function / homology
Function and homology information


saccharopepsin / microautophagy / cytoplasm to vacuole targeting by the Cvt pathway / oligosaccharide binding / pexophagy / fungal-type vacuole / proteolysis involved in protein catabolic process / macroautophagy / autophagy / disordered domain specific binding ...saccharopepsin / microautophagy / cytoplasm to vacuole targeting by the Cvt pathway / oligosaccharide binding / pexophagy / fungal-type vacuole / proteolysis involved in protein catabolic process / macroautophagy / autophagy / disordered domain specific binding / peptidase activity / aspartic-type endopeptidase activity / endoplasmic reticulum / protein-containing complex / mitochondrion
Similarity search - Function
Saccharopepsin / 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 ...Saccharopepsin / 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
CP-81,282, MOR-PHE-NLE-CHF-NME / Chem-2Z3 / Saccharopepsin
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å
AuthorsAguilar, C.F. / Badasso, M. / Dreyer, T. / Cronin, N.B. / Newman, M.P. / Cooper, J.B. / Hoover, D.J. / Wood, S.P. / Johnson, M.S. / Blundell, T.L.
CitationJournal: J.Mol.Biol. / Year: 1997
Title: The three-dimensional structure at 2.4 A resolution of glycosylated proteinase A from the lysosome-like vacuole of Saccharomyces cerevisiae.
Authors: Aguilar, C.F. / Cronin, N.B. / Badasso, M. / Dreyer, T. / Newman, M.P. / Cooper, J.B. / Hoover, D.J. / Wood, S.P. / Johnson, M.S. / Blundell, T.L.
History
DepositionApr 24, 1997Processing site: BNL
SupersessionOct 29, 1997ID: 1JXR
Revision 1.0Oct 29, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Dec 12, 2012Group: Other
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_chiral / software / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_database_status.process_site / _pdbx_molecule.asym_id / _pdbx_struct_assembly_gen.asym_id_list / _software.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 3, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEINASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5604
Polymers35,7751
Non-polymers1,7863
Water2,144119
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: PROTEINASE A
hetero molecules

A: PROTEINASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,1218
Polymers71,5492
Non-polymers3,5726
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+2/31
Buried area8380 Å2
ΔGint25 kcal/mol
Surface area26310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.700, 86.700, 110.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein PROTEINASE A / SACCHAROPEPSIN / YEAST ENDOPEPTIDASE A


Mass: 35774.551 Da / Num. of mol.: 1 / Mutation: L315I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P07267, saccharopepsin
#2: Polysaccharide alpha-D-mannopyranose-(1-2)-beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-2)-beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpb1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-2-3/a4-b1_b4-c1_c3-d1_d2-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][b-D-Manp]{[(2+1)][a-L-Idop]{}}}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-2Z3 / N-(morpholin-4-ylcarbonyl)-L-phenylalanyl-N-[(1R)-1-(cyclohexylmethyl)-3,3-difluoro-2,2-dihydroxy-4-(methylamino)-4-oxobutyl]-L-norleucinamide / CP-81,282


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 653.758 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H49F2N5O7 / References: CP-81,282, MOR-PHE-NLE-CHF-NME
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.3 Å3/Da / Density % sol: 63 %
Crystal grow
*PLUS
Method: vapor diffusion / Details: Badasso, M., (1993) J. Mol. Biol., 232, 701.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlenzyme1drop
210-25 %(w/v)PEG60001reservoir
30.01 Msodium acetate1reservoir

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1
DetectorDetector: IMAGE PLATE / Date: Nov 1, 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionNum. obs: 18325 / % possible obs: 95 % / Rmerge(I) obs: 0.07
Reflection
*PLUS
Highest resolution: 2.4 Å / Num. measured all: 84192

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Processing

Software
NameClassification
WEISdata collection
Agrovatadata reduction
RESTRAINrefinement
WEISdata reduction
Agrovatadata scaling
RefinementResolution: 2.4→10 Å
Details: LOOP RESIDUES A 140 - A 142 WERE MODELED STEREOCHEMICALLY.
RfactorNum. reflection
Rfree0.27 -
Rwork0.193 -
obs-18013
Displacement parametersBiso mean: 37.01 Å2
Refinement stepCycle: LAST / Resolution: 2.4→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2528 0 121 119 2768
Software
*PLUS
Name: RESTRAIN / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.193 / Rfactor Rfree: 0.27
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.0220.022
X-RAY DIFFRACTIONx_angle_d0.0550.037
X-RAY DIFFRACTIONx_planar_d0.0320.01
X-RAY DIFFRACTIONx_plane_restr0.0160.01
X-RAY DIFFRACTIONx_chiral_restr0.0240.02

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