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- PDB-1fmu: STRUCTURE OF NATIVE PROTEINASE A IN P3221 SPACE GROUP. -

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Basic information

Entry
Database: PDB / ID: 1fmu
TitleSTRUCTURE OF NATIVE PROTEINASE A IN P3221 SPACE GROUP.
ComponentsSACCHAROPEPSIN
KeywordsHYDROLASE / Proteinase A
Function / homology
Function and homology information


saccharopepsin / : / microautophagy / oligosaccharide binding / cytoplasm to vacuole targeting by the Cvt pathway / pexophagy / fungal-type vacuole / Neutrophil degranulation / proteolysis involved in protein catabolic process / macroautophagy ...saccharopepsin / : / microautophagy / oligosaccharide binding / cytoplasm to vacuole targeting by the Cvt pathway / pexophagy / fungal-type vacuole / Neutrophil degranulation / 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
alpha-D-mannopyranose / 2-acetamido-2-deoxy-alpha-D-glucopyranose / Saccharopepsin
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / Resolution: 2.7 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 Saccharomyces 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 / software
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_validate_chiral / pdbx_validate_close_contact / 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_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.ndb_seq_num / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SACCHAROPEPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3399
Polymers35,7751
Non-polymers1,5648
Water3,297183
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.606, 84.606, 108.703
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 SACCHAROPEPSIN / / PROTEINASE A


Mass: 35774.551 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P07267, saccharopepsin
#2: Sugar
ChemComp-MAN / alpha-D-mannopyranose / Mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


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
#4: Sugar ChemComp-NDG / 2-acetamido-2-deoxy-alpha-D-glucopyranose / N-Acetylglucosamine


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


Mass: 18.015 Da / Num. of mol.: 183 / 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: 3.14 Å3/Da / Density % sol: 60.8 %
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: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 6, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. all: 12565 / Num. obs: 12565 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Biso Wilson estimate: 54.9 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 25.7
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 5.02 % / Rmerge(I) obs: 0.386 / Num. unique all: 613 / % possible all: 96.5
Reflection
*PLUS
Num. measured all: 78120
Reflection shell
*PLUS
% possible obs: 96.5 % / Mean I/σ(I) obs: 3.9

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Processing

Software
NameVersionClassification
MAR345data collection
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementResolution: 2.7→19.71 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 3069059.21 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.271 554 5 %RANDOM
Rwork0.208 ---
all-12565 --
obs-11121 87.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 55.25 Å2 / ksol: 0.283 e/Å3
Displacement parametersBiso mean: 47.9 Å2
Baniso -1Baniso -2Baniso -3
1-7.98 Å28.03 Å20 Å2
2--7.98 Å20 Å2
3----15.96 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.48 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.7→19.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2475 0 105 183 2763
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d27.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.21
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.32 74 5.1 %
Rwork0.247 1376 -
obs--68.7 %
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: 2.7 Å / Rfactor Rfree: 0.2708 / Rfactor Rwork: 0.2071
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg27.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.21
LS refinement shell
*PLUS
Rfactor Rfree: 0.32

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