+Open data
-Basic information
Entry | Database: PDB / ID: 4a5g | |||||||||
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Title | Raphanus sativus anionic peroxidase. | |||||||||
Components | ANIONIC PEROXIDASE | |||||||||
Keywords | OXIDOREDUCTASE / GLYCOPROTEIN | |||||||||
Function / homology | Function and homology information peroxidase / hydrogen peroxide catabolic process / peroxidase activity / response to oxidative stress / heme binding / extracellular region / metal ion binding Similarity search - Function | |||||||||
Biological species | RAPHANUS SATIVUS (radish) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | |||||||||
Authors | Jimenez-Arroyo, N. / Valderrama, B. / Gil-Rodriguez, P. / Rojas-Trejo, S.P. / Rudino-Pinera, E. | |||||||||
Citation | Journal: To be Published Title: Crystallographic Structure of the Raphanus Sativus Anionic Peroxidase Authors: Gil-Rodriguez, P. / Jimenez-Arroyo, N. / Rojas-Trejo, S.P. / Rudino-Pinera, E. / Valderrama, B. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4a5g.cif.gz | 167.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4a5g.ent.gz | 132.2 KB | Display | PDB format |
PDBx/mmJSON format | 4a5g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a5/4a5g ftp://data.pdbj.org/pub/pdb/validation_reports/a5/4a5g | HTTPS FTP |
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-Related structure data
Related structure data | 1pa2S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 31965.322 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) RAPHANUS SATIVUS (radish) / Tissue: ROOT / References: UniProt: K7N5L9*PLUS, peroxidase |
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-Sugars , 9 types, 14 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #4: Polysaccharide | alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #5: Polysaccharide | Source method: isolated from a genetically manipulated source #6: Polysaccharide | beta-D-xylopyranose-(1-2)-[beta-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...beta-D-xylopyranose-(1-2)-[beta-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #7: 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 #8: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-3) ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #9: Polysaccharide | alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta- ...alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #12: Sugar | ChemComp-NAG / |
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-Non-polymers , 5 types, 714 molecules
#10: Chemical | #11: Chemical | ChemComp-CA / #13: Chemical | ChemComp-1PE / #14: Chemical | ChemComp-PG0 / | #15: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | POLYETHYLENE GLYCOL 6000 FRAGMENT (PG0 AND 1PE): THESE COORDINATES CORRESPOND TO VISIBLE FRAGMENTS ...POLYETHYLE |
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Sequence details | THE SEQUENCE OF RAPHANUS SATIVUS ANIONIC PEROXIDASE HAS NEVER BEEN RELEASED. HOWEVER THE SEQUENCE ...THE SEQUENCE OF RAPHANUS SATIVUS ANIONIC PEROXIDASE |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.58 % Description: PART OF THE PHASES WERE OBTAINED FROM THE ANOMALOUS SIGNAL COMING FROM THE IRON ATOMS AT THE HEME GROUP |
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Crystal grow | pH: 6.5 Details: THE PROTEIN CONCENTRATION WAS 50 MG/ML. THE PRECIPITANT SOLUTION COMPRISES 20% PEG 6000, 20% PEG 200, 100 MM MES PH 6.5. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1.7329 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Mar 20, 2010 Details: DOUBLE CRYSTAL CHANNEL CUT, SI(111), 1M LONG RH COATED TOROIDAL MIRROR FOR VERTICAL AND HORIZONTAL FOCUSING. |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.7329 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→40 Å / Num. obs: 51917 / % possible obs: 98.6 % / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 27.82 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 21.6 |
Reflection shell | Resolution: 2.05→2.09 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 3.53 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1PA2 Resolution: 2.05→35.287 Å / SU ML: 0.56 / σ(F): 1.34 / Phase error: 15.58 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.53 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→35.287 Å
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Refine LS restraints |
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LS refinement shell |
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