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Yorodumi- PDB-2wea: ACID PROTEINASE (PENICILLOPEPSIN) (E.C.3.4.23.20) COMPLEX WITH PH... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wea | |||||||||
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Title | ACID PROTEINASE (PENICILLOPEPSIN) (E.C.3.4.23.20) COMPLEX WITH PHOSPHONATE INHIBITOR: METHYL[CYCLO-7[(2R)-((N-VALYL) AMINO)-2-(HYDROXYL-(1S)-1-METHYOXYCARBONYL-2-PHENYLETHOXY) PHOSPHINYLOXY-ETHYL]-1-NAPHTHALENEACETAMIDE], SODIUM SALT | |||||||||
Components | PENICILLOPEPSIN | |||||||||
Keywords | HYDROLASE / PENICILLOPEPSIN / PHOSPHONATE INHIBITOR | |||||||||
Function / homology | Function and homology information penicillopepsin / aspartic-type endopeptidase activity / proteolysis / extracellular region Similarity search - Function | |||||||||
Biological species | Penicillium janthinellum (fungus) | |||||||||
Method | X-RAY DIFFRACTION / DIFFERENCE FOURIER METHOD / Resolution: 1.25 Å | |||||||||
Authors | Ding, J. / Fraser, M.E. / James, M.N.G. | |||||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 1998 Title: Macrocyclic Inhibitors of Penicillopepsin. II. X-Ray Crystallographic Analyses of Penicillopepsin Complexed with a P3-P1 Macrocyclic Peptidyl Inhibitor and with its Two Acyclic Analogues Authors: Ding, J. / Fraser, M.E. / Meyer, J.H. / Bartlett, P.A. / James, M.N.G. #1: Journal: To be Published Title: Macrocyclic Inhibitors of Penicillopepsin. I. Design, Synthesis, and Evaluation of an Inhibitor Bridged between P1 and P3 Authors: Meyer, J.H. / Bartlett, P.A. #2: Journal: Biochemistry / Year: 1992 Title: Crystallographic Analysis of Transition-State Mimics Bound to Penicillopepsin: Phosphorus-Containing Peptide Analogues Authors: Fraser, M.E. / Strynadka, N.C. / Bartlett, P.A. / Hanson, J.E. / James, M.N. #3: Journal: Biochemistry / Year: 1992 Title: Crystallographic Analysis of Transition State Mimics Bound to Penicillopepsin: Difluorostatine-and Difluorostatone-Containing Peptides Authors: James, M.N. / Sielecki, A.R. / Hayakawa, K. / Gelb, M.H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wea.cif.gz | 82.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wea.ent.gz | 63.2 KB | Display | PDB format |
PDBx/mmJSON format | 2wea.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2wea_validation.pdf.gz | 495.8 KB | Display | wwPDB validaton report |
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Full document | 2wea_full_validation.pdf.gz | 496.9 KB | Display | |
Data in XML | 2wea_validation.xml.gz | 8.4 KB | Display | |
Data in CIF | 2wea_validation.cif.gz | 15.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/we/2wea ftp://data.pdbj.org/pub/pdb/validation_reports/we/2wea | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 33468.809 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Penicillium janthinellum (fungus) / References: UniProt: P00798, penicillopepsin | ||||||
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#2: Sugar | #3: Chemical | ChemComp-SO4 / | #4: Chemical | ChemComp-PP6 / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 36.81 % | ||||||||||||||||||||||||
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Crystal grow | pH: 4.4 / Details: 0.1M NAC2H3O2 PH=4.4 35-40% SATURATED (NH4)2SO4 | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18-22 ℃ / Method: vapor diffusion, hanging dropDetails: used macroseeding, Fraser, M.E., (1992) Biochemistry, 31, 5201. | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ROTATING ANODE / Type: OTHER / Wavelength: 1.5418 |
Detector | Type: SIEMENS-NICOLET X100 / Detector: AREA DETECTOR / Date: Mar 22, 1997 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→40 Å / Num. obs: 58629 / % possible obs: 82.22 % / Observed criterion σ(I): 0 / Redundancy: 3.47 % / Biso Wilson estimate: 10.427 Å2 / Rmerge(I) obs: 0.0595 / Net I/σ(I): 41.28 |
Reflection shell | Resolution: 1.25→1.29 Å / Redundancy: 2.05 % / Rmerge(I) obs: 0.148 / Mean I/σ(I) obs: 5.18 / % possible all: 40.47 |
Reflection | *PLUS Observed criterion σ(I): 2 / Num. measured all: 203415 |
Reflection shell | *PLUS % possible obs: 40.47 % |
-Processing
Software |
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Refinement | Method to determine structure: DIFFERENCE FOURIER METHOD / Resolution: 1.25→40 Å Isotropic thermal model: CSDX_PROTGEO.DAT, OTHERGEO.DAT, CPPP6GEO.DAT, SEMTHMGEO.DAT σ(F): 2 Stereochemistry target values: CSDX_PROTGEO.DAT, OTHERGEO.DAT, CPPP6GEO.DAT, SEMTHMGEO.DAT, CONTACT.DAT Details: X-PLOR AND TNT ESD FROM SIGMAA (A) : 0.138904 UNCERTAINTY IN RMS ERROR SQUARED : 0.001516
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Solvent computation | Solvent model: TNT / Bsol: 441.6 Å2 / ksol: 1.002 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.25→40 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Version: 5E / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor all: 0.155 / Rfactor Rfree: 0.192 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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