+Open data
-Basic information
Entry | Database: PDB / ID: 1atj | ||||||
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Title | RECOMBINANT HORSERADISH PEROXIDASE C1A | ||||||
Components | PEROXIDASE C1A | ||||||
Keywords | OXIDOREDUCTASE / PEROXIDASE / GLYCOPROTEIN | ||||||
Function / homology | Function and homology information lactoperoxidase activity / peroxidase / vacuole / hydrogen peroxide catabolic process / response to oxidative stress / heme binding / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Armoracia rusticana (horseradish) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Gajhede, M. / Schuller, D.J. / Henriksen, A. / Smith, A.T. / Poulos, T.L. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1997 Title: Crystal structure of horseradish peroxidase C at 2.15 A resolution. Authors: Gajhede, M. / Schuller, D.J. / Henriksen, A. / Smith, A.T. / Poulos, T.L. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1995 Title: Crystallization and Preliminary X-Ray Studies of Recombinant Horseradish Peroxidase Authors: Henriksen, A. / Gajhede, M. / Baker, P. / Smith, A.T. / Burke, J.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1atj.cif.gz | 439.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1atj.ent.gz | 365.2 KB | Display | PDB format |
PDBx/mmJSON format | 1atj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/at/1atj ftp://data.pdbj.org/pub/pdb/validation_reports/at/1atj | HTTPS FTP |
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-Related structure data
Related structure data | 1schS 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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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 33746.961 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Armoracia rusticana (horseradish) / Production host: Escherichia coli (E. coli) / References: UniProt: P00433, peroxidase #2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-HEM / #4: Water | ChemComp-HOH / | |
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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: 2.04 Å3/Da / Density % sol: 39 % | ||||||||||||||||||||
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Crystal grow | pH: 6.5 Details: 16% (W/V) PEG 4000, 0.2 M ZINC ACETATE AND 0.1 M CACODYLATE BUFFER, PH 6.5 | ||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion / Details: Braithwaite, A., (1976) J. Mol. Biol., 106, 229. | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Aug 1, 1995 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→100 Å / Num. obs: 73216 / % possible obs: 83.6 % / Observed criterion σ(I): 0 / Redundancy: 1.7 % / Biso Wilson estimate: 12.8 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.07 |
Reflection shell | Resolution: 2.15→2.9 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.4 / Rsym value: 0.4 / % possible all: 65.4 |
Reflection | *PLUS Num. measured all: 142833 |
Reflection shell | *PLUS Lowest resolution: 2.19 Å / % possible obs: 65.4 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1SCH Resolution: 2.15→100 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Displacement parameters | Biso mean: 24.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.15→100 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.15→2.23 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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