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Yorodumi- PDB-7h5j: Crystal structure of endothiapepsin IS_cryo1 in complex with AC40... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7h5j | |||||||||
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Title | Crystal structure of endothiapepsin IS_cryo1 in complex with AC40075 at 100 K | |||||||||
Components | Endothiapepsin | |||||||||
Keywords | HYDROLASE / Endopeptidase / room temperature | |||||||||
Function / homology | Function and homology information 4-hydroxy-3-polyprenylbenzoate decarboxylase / 3-octaprenyl-4-hydroxybenzoate carboxy-lyase activity / ferulate metabolic process / cinnamic acid catabolic process / ubiquinone biosynthetic process / metal ion binding / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | Cryphonectria parasitica (chestnut blight fungus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å | |||||||||
Authors | Huang, C.-Y. / Aumonier, S. / Olieric, V. / Wang, M. | |||||||||
Funding support | Switzerland, European Union, 2items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2024 Title: Cryo2RT: a high-throughput method for room-temperature macromolecular crystallography from cryocooled crystals. Authors: Huang, C.Y. / Aumonier, S. / Olieric, V. / Wang, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7h5j.cif.gz | 85.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7h5j.ent.gz | 62.7 KB | Display | PDB format |
PDBx/mmJSON format | 7h5j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7h5j_validation.pdf.gz | 720.3 KB | Display | wwPDB validaton report |
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Full document | 7h5j_full_validation.pdf.gz | 720.9 KB | Display | |
Data in XML | 7h5j_validation.xml.gz | 18.6 KB | Display | |
Data in CIF | 7h5j_validation.cif.gz | 29.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h5/7h5j ftp://data.pdbj.org/pub/pdb/validation_reports/h5/7h5j | HTTPS FTP |
-Group deposition
ID | G_1002290 (30 entries) |
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Title | A High-Throughput Method for Room-Temperature Macromolecular Crystallography from Frozen Crystals |
Type | undefined |
Description | A High-Throughput Method for Room-Temperature Macromolecular Crystallography from Frozen Crystals |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-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, EC: 3.4.23.22 | ||||||
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#2: Chemical | ChemComp-ACT / | ||||||
#3: Chemical | ChemComp-DMS / #4: Chemical | ChemComp-EMR / | #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: 2.47 Å3/Da / Density % sol: 50.21 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.1 M ammonium acetate, 0.1 M sodium acetate pH 4.6, and 26 - 30% (v/v) PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 15, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→38.82 Å / Num. obs: 19868 / % possible obs: 91.7 % / Redundancy: 12.28 % / Biso Wilson estimate: 24.79 Å2 / Rmerge F all: 0.15 / CC1/2: 0.99 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 12.01 % / Rmerge F all: 0.52 / Num. unique obs: 1522 / CC1/2: 0.92 / Net I/σ(I) all: 5.01 / % possible all: 94.8 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→20.91 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.912 / SU R Cruickshank DPI: 0.205 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.247 / SU Rfree Blow DPI: 0.176 / SU Rfree Cruickshank DPI: 0.166
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Displacement parameters | Biso max: 89.92 Å2 / Biso mean: 25.14 Å2 / Biso min: 11.78 Å2
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Refine analyze | Luzzati coordinate error obs: 0.21 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2→20.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.01 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
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