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- PDB-1fmx: STRUCTURE OF NATIVE PROTEINASE A IN THE SPACE GROUP P21 -

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Basic information

Entry
Database: PDB / ID: 1fmx
TitleSTRUCTURE OF NATIVE PROTEINASE A IN THE SPACE GROUP P21
ComponentsSACCHAROPEPSIN
KeywordsHYDROLASE / proteinase A
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
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.61 Å
AuthorsGustchina, A. / Li, M. / Phylip, L.H. / Lees, W.E. / Kay, J. / Wlodawer, A.
Citation
Journal: Biochem.Biophys.Res.Commun. / Year: 2002
Title: An unusual orientation for Tyr75 in the active site of the aspartic proteinase from Saccharomyces cerevisiae.
Authors: Gustchina, A. / Li, M. / Phylip, L.H. / Lees, W.E. / Kay, J. / Wlodawer, A.
#1: Journal: Nat.Struct.Biol. / Year: 2000
Title: The aspartic proteinase from A. Cerevisiae folds its own inhibitor into a helix
Authors: Li, M. / Phylip, L. / Lees, W. / Winther, J. / Dunn, B. / Wlodawer, A. / Kay, J. / Gustchina, A.
History
DepositionAug 18, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 4, 2017Group: Advisory / Refinement description
Category: pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / software
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / 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.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _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 2.1Oct 30, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _chem_comp.pdbx_synonyms / _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: SACCHAROPEPSIN
B: SACCHAROPEPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,0026
Polymers71,5492
Non-polymers1,4534
Water3,549197
1
A: SACCHAROPEPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5823
Polymers35,7751
Non-polymers8082
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SACCHAROPEPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4203
Polymers35,7751
Non-polymers6462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.964, 49.074, 94.685
Angle α, β, γ (deg.)90.00, 96.50, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein SACCHAROPEPSIN / PROTEINASE A


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


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#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.: 2
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.: 197 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 54.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG 1500, Ammonium Sulfate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 6.6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
128 %PEG15001reservoir
20.2 Mammonium sulfate1reservoir
30.1 MMES1reservoirpH6.0
420 mMMES1droppH6.6
55 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 1.5418
DetectorType: ADSC QUANTUM / Detector: CCD / Date: Feb 17, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. all: 22963 / Num. obs: 22963 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 45.9 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 14.2
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.562 / Num. unique all: 2224 / % possible all: 97.6
Reflection
*PLUS
Num. measured all: 75834
Reflection shell
*PLUS
% possible obs: 97.6 % / Mean I/σ(I) obs: 2.1

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementResolution: 2.61→24.99 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 2089705.79 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): -3 / Stereochemistry target values: ENGH & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.279 1038 4.9 %RANDOM
Rwork0.205 ---
obs0.205 21354 91.3 %-
all-22963 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 60.63 Å2 / ksol: 0.269 e/Å3
Displacement parametersBiso mean: 54.4 Å2
Baniso -1Baniso -2Baniso -3
1--4.66 Å20 Å210.18 Å2
2--6.86 Å20 Å2
3----2.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.54 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2.61→24.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4996 0 95 197 5288
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg2
X-RAY DIFFRACTIONc_dihedral_angle_d26.6
X-RAY DIFFRACTIONc_improper_angle_d1.33
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.38 129 4.9 %
Rwork0.294 2518 -
obs--68 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2CARBOHYDRATE.PARAMCARBOHYDRATE.TOP
X-RAY DIFFRACTION3WATER.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Refinement
*PLUS
Highest resolution: 2.6 Å / Rfactor Rfree: 0.2805 / Rfactor Rwork: 0.2044
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.33
LS refinement shell
*PLUS
Rfactor Rfree: 0.38

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