+Open data
-Basic information
Entry | Database: PDB / ID: 8pxi | ||||||
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Title | Crystal structure of Endothiapepsin soaked with FRG283 | ||||||
Components | Endothiapepsin | ||||||
Keywords | HYDROLASE / Endothiapepsin / ligand complex | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Cryphonectria parasitica (chestnut blight fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å | ||||||
Authors | Mueller, J.M. / Eckelt, S. / Klebe, G. / Glinca, S. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Crystal structures of Endothiapepsin with ligands derived from merged fragment hits Authors: Mueller, J.M. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2012 Title: Towards automated crystallographic structure refinement with phenix.refine. Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D. #2: Journal: Acta Crystallogr D Struct Biol / Year: 2019 Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams / Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8pxi.cif.gz | 174.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8pxi.ent.gz | 113.6 KB | Display | PDB format |
PDBx/mmJSON format | 8pxi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8pxi_validation.pdf.gz | 704.4 KB | Display | wwPDB validaton report |
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Full document | 8pxi_full_validation.pdf.gz | 704.3 KB | Display | |
Data in XML | 8pxi_validation.xml.gz | 15.7 KB | Display | |
Data in CIF | 8pxi_validation.cif.gz | 23.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/px/8pxi ftp://data.pdbj.org/pub/pdb/validation_reports/px/8pxi | HTTPS FTP |
-Related structure data
Related structure data | 8q0vC 8q0wC 8q0xC 8q0yC 8q0zC 8q10C 8q11C 8q12C 8q13C 8q14C C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 33813.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Cryphonectria parasitica (chestnut blight fungus) References: UniProt: P11838, endothiapepsin | ||||||
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#2: Chemical | ChemComp-MPD / ( | ||||||
#3: Chemical | #4: Chemical | ChemComp-D8V / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.52 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: Protein at 5 mg/mL in 100 mM ammoniumacetate pH 4.6, reservoir: 100 mM ammoniumacetate, 100 mM sodium acetate pH 4.6, 24 % PEG4000, 292 K, 2+2 yL drops over 1 mL reservoir, streak seeding |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 0.68879 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 24, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.68879 Å / Relative weight: 1 |
Reflection | Resolution: 1.199→50 Å / Num. obs: 98083 / % possible obs: 98.6 % / Redundancy: 3.52 % / Biso Wilson estimate: 14.83 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.053 / Net I/σ(I): 11.96 |
Reflection shell | Resolution: 1.2→1.27 Å / Mean I/σ(I) obs: 1.05 / Num. unique obs: 15864 / CC1/2: 0.608 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→40.73 Å / SU ML: 0.1538 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.7773 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.02 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.2→40.73 Å
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Refine LS restraints |
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LS refinement shell |
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