+Open data
-Basic information
Entry | Database: PDB / ID: 1pa2 | ||||||
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Title | ARABIDOPSIS THALIANA PEROXIDASE A2 | ||||||
Components | PEROXIDASE | ||||||
Keywords | OXIDOREDUCTASE / PEROXIDASE | ||||||
Function / homology | Function and homology information defense response to nematode / flower development / lactoperoxidase activity / peroxidase / hydrogen peroxide catabolic process / response to oxidative stress / heme binding / Golgi apparatus / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | ||||||
Authors | Henriksen, A. | ||||||
Citation | Journal: Plant Mol.Biol. / Year: 2000 Title: Arabidopsis ATP A2 peroxidase. Expression and high-resolution structure of a plant peroxidase with implications for lignification. Authors: Ostergaard, L. / Teilum, K. / Mirza, O. / Mattsson, O. / Petersen, M. / Welinder, K.G. / Mundy, J. / Gajhede, M. / Henriksen, A. #1: Journal: FEBS Lett. / Year: 1996 Title: Structure and Organ Specificity of an Anionic Peroxidase from Arabidopsis Thaliana Cell Suspension Culture Authors: Ostergaard, L. / Abelskov, A.K. / Mattsson, O. / Welinder, K.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1pa2.cif.gz | 122.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pa2.ent.gz | 87.7 KB | Display | PDB format |
PDBx/mmJSON format | 1pa2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pa/1pa2 ftp://data.pdbj.org/pub/pdb/validation_reports/pa/1pa2 | HTTPS FTP |
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-Related structure data
Related structure data | 1atjS 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
#1: Protein | Mass: 32085.516 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Production host: Escherichia coli (E. coli) / References: UniProt: Q42578, peroxidase | ||||||
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#2: Chemical | #3: Chemical | ChemComp-MG / | #4: Chemical | ChemComp-HEM / | #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: 2.16 Å3/Da / Density % sol: 42.99 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 / Details: pH 6.5 | ||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 0.97 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 1, 1998 / Details: VERTICALLY FOCUSING CYLINDRICAL MIRROR |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→99 Å / Num. obs: 49745 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Rsym value: 0.058 / Net I/σ(I): 19.1 |
Reflection shell | Resolution: 1.45→1.51 Å / Redundancy: 4 % / Mean I/σ(I) obs: 8.4 / Rsym value: 0.202 / % possible all: 99 |
Reflection | *PLUS Lowest resolution: 99 Å / % possible obs: 99 % / Num. measured all: 280003 / Rmerge(I) obs: 0.058 |
Reflection shell | *PLUS % possible obs: 99 % / Num. unique obs: 5403 / Rmerge(I) obs: 0.243 / Mean I/σ(I) obs: 6.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ATJ Resolution: 1.45→99 Å / Num. parameters: 11562 / Num. restraintsaints: 9824 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-2 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 29 / Occupancy sum hydrogen: 2187 / Occupancy sum non hydrogen: 2775 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.45→99 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-96 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 99 Å / σ(F): 4 / % reflection Rfree: 5 % / Rfactor all: 0.1477 / Rfactor obs: 0.1398 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |