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Yorodumi- PDB-7dlh: Crystallization of Cationic Peroxidase from Proso Millet and Iden... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7dlh | ||||||
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Title | Crystallization of Cationic Peroxidase from Proso Millet and Identification of Its Phosphatase Active Sites | ||||||
Components | peroxidase | ||||||
Keywords | OXIDOREDUCTASE / Proso millet peroxidase | ||||||
Function / homology | alpha-L-fucopyranose / PROTOPORPHYRIN IX CONTAINING FE Function and homology information | ||||||
Biological species | Panicum miliaceum (broom millet) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.789 Å | ||||||
Authors | Cui, x.d. / Wang, t.f. / Wang, k. | ||||||
Citation | Journal: To Be Published Title: Crystallization of Cationic Peroxidase from Proso Millet and Identification of Its Phosphatase Active Sites Authors: Cui, x.d. / Wang, t.f. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7dlh.cif.gz | 88.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7dlh.ent.gz | 62.7 KB | Display | PDB format |
PDBx/mmJSON format | 7dlh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7dlh_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 7dlh_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 7dlh_validation.xml.gz | 18.2 KB | Display | |
Data in CIF | 7dlh_validation.cif.gz | 27.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dl/7dlh ftp://data.pdbj.org/pub/pdb/validation_reports/dl/7dlh | HTTPS FTP |
-Related structure data
Related structure data | 5aogS S: Starting model for refinement |
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Similar structure data |
-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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 36295.078 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Panicum miliaceum (broom millet) / Production host: Panicum miliaceum (broom millet) |
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-Sugars , 3 types, 3 molecules
#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#3: Polysaccharide | alpha-D-mannopyranose-(2-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy- ...alpha-D-mannopyranose-(2-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source |
#5: Sugar | ChemComp-FUC / |
-Non-polymers , 6 types, 369 molecules
#4: Chemical | ChemComp-HEM / | ||
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#6: Chemical | ChemComp-CA / | ||
#7: Chemical | ChemComp-NA / | ||
#8: Chemical | ChemComp-GOL / | ||
#9: Chemical | #10: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.54 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 0.1 mol/L Tris-HCl, pH 8.0, 0.2 mol/L MgCl2, and 25%(w/v) PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.978 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 2, 2018 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.789→50 Å / Num. obs: 33291 / % possible obs: 98.6 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.138 / Rpim(I) all: 0.078 / Rrim(I) all: 0.16 / Χ2: 0.51 / Net I/σ(I): 3.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5AOG Resolution: 1.789→39.641 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 19.02 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 70.1 Å2 / Biso mean: 16.1507 Å2 / Biso min: 5.43 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.789→39.641 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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