+Open data
-Basic information
Entry | Database: PDB / ID: 1oag | ||||||
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Title | Ascorbate peroxidase from soybean cytosol | ||||||
Components | ASCORBATE PEROXIDASE | ||||||
Keywords | OXIDOREDUCTASE / HEME PEROXIDASE / PEROXIDE SCAVENGE / ASCORBATE PEROXIDASE | ||||||
Function / homology | Function and homology information L-ascorbate peroxidase / L-ascorbate peroxidase activity / cellular response to oxidative stress / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | GLYCINE MAX (soybean) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Sharp, K.H. / Raven, E.L. / Moody, P.C.E. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2003 Title: Crystal Structure of the Ascorbate Peroxidase-Ascorbate Complex Authors: Sharp, K.H. / Mewies, M. / Moody, P.C.E. / Raven, E.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1oag.cif.gz | 75.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1oag.ent.gz | 54.5 KB | Display | PDB format |
PDBx/mmJSON format | 1oag.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oa/1oag ftp://data.pdbj.org/pub/pdb/validation_reports/oa/1oag | HTTPS FTP |
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-Related structure data
Related structure data | 1oafC 1apxS C: citing same article (ref.) 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
#1: Protein | Mass: 28361.904 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) GLYCINE MAX (soybean) / Description: N-TERMINAL 6-HIS TAG / Plasmid: PAPX4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): SG13009 / References: UniProt: Q43758, L-ascorbate peroxidase |
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#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-SO4 / |
#4: 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: 2.3 Å3/Da / Density % sol: 46 % | ||||||||||||||||||||||||
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Crystal grow | pH: 8.3 / Details: 2.25M LI2SO4, 0.1M HEPES, PH8.3, pH 8.30 | ||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting 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: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.811 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Aug 13, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.811 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→40 Å / Num. obs: 26092 / % possible obs: 99.3 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 1.75→1.8 Å / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2.4 / % possible all: 99.3 |
Reflection | *PLUS Lowest resolution: 57.74 Å / Num. measured all: 92501 |
Reflection shell | *PLUS % possible obs: 99.3 % / Rmerge(I) obs: 0.32 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1APX Resolution: 1.75→57.74 Å / SU B: 1.882 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.099 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUE 1 AND THE N-TERMINAL HIS-TAG ARE NOT VISIBLE
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Displacement parameters | Biso mean: 16.44 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→57.74 Å
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Refinement | *PLUS Rfactor Rfree: 0.182 / Rfactor Rwork: 0.178 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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