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- PDB-3app: STRUCTURE AND REFINEMENT OF PENICILLOPEPSIN AT 1.8 ANGSTROMS RESO... -

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Basic information

Entry
Database: PDB / ID: 3app
TitleSTRUCTURE AND REFINEMENT OF PENICILLOPEPSIN AT 1.8 ANGSTROMS RESOLUTION
ComponentsPENICILLOPEPSIN
KeywordsHYDROLASE (ACID PROTEINASE)
Function / homology
Function and homology information


penicillopepsin / aspartic-type endopeptidase activity / proteolysis / extracellular region
Similarity search - Function
Aspergillopepsin-like catalytic domain / 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 ...Aspergillopepsin-like catalytic domain / 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 speciesPenicillium janthinellum (fungus)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsSielecki, A.R. / James, M.N.G.
Citation
Journal: J.Mol.Biol. / Year: 1983
Title: Structure and refinement of penicillopepsin at 1.8 A resolution.
Authors: James, M.N. / Sielecki, A.R.
#1: Journal: Biological Macromolecules and Assemblies / Year: 1987
Title: Aspartic Proteinases and Their Catalytic Pathway
Authors: James, M.N.G. / Sielecki, A.R.
#2: Journal: Biochemistry / Year: 1985
Title: Stereochemical Analysis of Peptide Bond Hydrolysis Catalyzed by the Aspartic Proteinase Penicillopepsin
Authors: James, M.N.G. / Sielecki, A.R.
#3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1982
Title: Conformational Flexibility in the Active Sites of Aspartyl Proteinases Revealed by a Pepstatin Fragment Binding to Penicillopepsin
Authors: James, M.N.G. / Sielecki, A. / Salituro, F. / Rich, D.H. / Hofmann, T.
#4: Journal: STRUCTURAL STUDIES ON MOLECULES OF BIOLOGICA INTERESTL
Year: 1981
Title: The Tertiary Structure of Penicillopepsin. Towards a Catalytic Mechanism for Acid Proteases
Authors: James, M.N.G. / Hsu, I-N. / Hofmann, T. / Sielecki, A.R.
#5: Journal: Can.J.Biochem. / Year: 1980
Title: An X-Ray Crystallographic Approach to Enzyme Structure and Function
Authors: James, M.N.G.
#6: Journal: Nature / Year: 1978
Title: Structural Evidence for Gene Duplication in the Evolution of the Acid Proteases
Authors: Tang, J. / James, M.N.G. / Hsu, I.N. / Jenkins, J.A. / Blundell, T.L.
#7: Journal: Nature / Year: 1977
Title: Mechanism of Acid Protease Catalysis Based on the Crystal Structure of Penicillopepsin
Authors: James, M.N.G. / Hsu, I.-N. / Delbaere, L.T.J.
#8: Journal: Nature / Year: 1977
Title: Penicillopepsin from Penicillium Janthinellum Crystal Structure at 2.8 Angstroms and Sequence Homology with Porcine Pepsin
Authors: Hsu, I.-N. / Delbaere, L.T.J. / James, M.N.G. / Hofmann, T.
#9: Journal: Adv.Exp.Med.Biol. / Year: 1977
Title: Penicillopepsin. 2.8 Angstroms Structure, Active Site Conformation and Mechanistic Implications
Authors: Hsu, I-N. / Delbaere, L.T.J. / James, M.N.G. / Hofmann, T.
#10: Journal: Biochem.Biophys.Res.Commun. / Year: 1976
Title: The Crystal Structure of Penicillopepsin at 6 Angstroms Resolution
Authors: Hsu, I-N. / Hofmann, T. / Nyburg, S.C. / James, M.N.G.
History
DepositionNov 27, 1990Processing site: BNL
SupersessionJan 15, 1991ID: 2APP
Revision 1.0Jan 15, 1991Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 650HELIX THE HYDROGEN-BONDING PATTERN AND THE VALUES OF THE PHI, PSI ANGLES WERE USED TO IDENTIFY THE ...HELIX THE HYDROGEN-BONDING PATTERN AND THE VALUES OF THE PHI, PSI ANGLES WERE USED TO IDENTIFY THE SEVERAL SHORT SEGMENTS OF ALPHA-HELICAL CONFORMATION. THERE ARE SIX ALPHA-HELICES, RANGING IN LENGTH FROM 1 TO 2.5 TURNS. FOUR OF THEM HAVE ASSOCIATED 3/10 HELICES INITIATING AND/OR TERMINATING THEM. THE TWO SINGLE TURNS OF ALPHA-HELIX, PRO 59 - GLY 63, ASP 239 - GLY 243, ARE IRREGULAR. THEIR ASSIGNMENT AS ALPHA-HELICAL WAS MADE ON THE BASIS OF GOOD 5-1 HYDROGEN BONDING. THE SPECIFICS ON 3/10 HELICES ARE AS FOLLOWS H1. ASN 58 - ALA 61 3/10 HELIX TYPE III H2. SER 109 - PHE 112 3/10 HELIX TYPE III PHE 112 - ASP 115 3/10 HELIX TYPE III H3. VAL 144 - SER 147 3/10 HELIX TYPE III LYS 145 - LEU 148 3/10 HELIX TYPE I H4. ASP 222 - VAL 225 3/10 HELIX TYPE III TYR 229 - GLN 232 3/10 HELIX TYPE III TYR 230 - VAL 233 3/10 HELIX TYPE I H6. GLY 299 - PHE 302 3/10 HELIX TYPE III PHE 302 - SER 305 3/10 HELIX TYPE III LEU 303 - GLN 306 3/10 HELIX TYPE I

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PENICILLOPEPSIN


Theoretical massNumber of molelcules
Total (without water)33,4691
Polymers33,4691
Non-polymers00
Water5,729318
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.370, 46.640, 65.470
Angle α, β, γ (deg.)90.00, 115.40, 90.00
Int Tables number5
Space group name H-MC121
Atom site foot note1: THE REGION FROM SER 277 TO SER 281 IS POORLY ORDERED IN THE ELECTRON DENSITY MAP AT CYCLE 86 (SEE FIGURE 6C IN THE PAPER CITED AS REFERENCE 1 ABOVE).
2: RESIDUES 134 AND 315 ARE CIS-PROLINES.

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Components

#1: Protein PENICILLOPEPSIN


Mass: 33468.809 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Penicillium janthinellum (fungus) / References: UniProt: P00798, penicillopepsin
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 318 / 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

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Sample preparation

CrystalDensity Matthews: 2.01 Å3/Da / Density % sol: 38.67 %
Crystal grow
*PLUS
pH: 4.4 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlenzyme11
21.4 Mammonium sulphate11
30.1 Msodium acetate11

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.8→8 Å / σ(I): 3
Details: THE REGION FROM SER 277 TO SER 281 IS POORLY ORDERED IN THE ELECTRON DENSITY
RfactorNum. reflection
obs0.126 18168
Refinement stepCycle: LAST / Resolution: 1.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2366 0 0 318 2684
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.126
Solvent computation
*PLUS
Displacement parameters
*PLUS

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