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Yorodumi- PDB-1kzm: Distal Heme Pocket Mutant (R38S/H42E) of Recombinant Horseradish ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kzm | ||||||
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Title | Distal Heme Pocket Mutant (R38S/H42E) of Recombinant Horseradish Peroxidase C (HRP C). | ||||||
Components | Peroxidase C1A | ||||||
Keywords | OXIDOREDUCTASE / Peroxidase / Horseradish / Heme enzyme / Mutant | ||||||
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 / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 Å | ||||||
Authors | Meno, K. / Henriksen, A. / Smith, A.T. / Gajhede, M. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2002 Title: Structural analysis of the two horseradish peroxidase catalytic residue variants H42E and R38S/H42E: implications for the catalytic cycle. Authors: Meno, K. / Jennings, S. / Smith, A.T. / Henriksen, A. / Gajhede, M. #1: 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. #2: Journal: Biochemistry / Year: 1998 Title: Structural interactions between horseradish peroxidase C and the substrate benzhydroxamic acid determined by X-ray crystallography. Authors: Henriksen, A. / Schuller, D.J. / Meno, K. / Welinder, K.G. / Smith, A.T. / Gajhede, M. #3: Journal: J.Biol.Chem. / Year: 1999 Title: The structures of the horseradish peroxidase C-ferulic acid complex and the ternary complex with cyanide suggest how peroxidases oxidize small phenolic substrates. Authors: Henriksen, A. / Smith, A.T. / Gajhede, M. | ||||||
History |
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Remark 12 | THE NORMAL S-S BRIDGE BETWEEN CYS97 AND CYS301 HAS BEEN BROKEN AS A RESULT OF RADIATION DAMAGE. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kzm.cif.gz | 84.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kzm.ent.gz | 60.5 KB | Display | PDB format |
PDBx/mmJSON format | 1kzm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kz/1kzm ftp://data.pdbj.org/pub/pdb/validation_reports/kz/1kzm | HTTPS FTP |
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-Related structure data
Related structure data | 4atjC 6atjS S: Starting model for refinement C: citing same article (ref.) |
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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: 33868.992 Da / Num. of mol.: 1 / Fragment: Horseradish Peroxidase C1A (HRP C) / Mutation: R38S/H42E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Armoracia rusticana (horseradish) / Gene: PRXC1A or HPRC1 / Production host: Escherichia coli (E. coli) / References: UniProt: P00433, peroxidase | ||||||
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#2: Chemical | #3: Chemical | ChemComp-CAC / | #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: 2.33 Å3/Da / Density % sol: 47.16 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG-8000, calcium acetate, cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 283K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Type: ESRF / Wavelength: 0.934 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 8, 1999 |
Radiation | Monochromator: Standard / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. obs: 21058 / % possible obs: 95.1 % / Observed criterion σ(I): -3 / Redundancy: 5.8 % / Biso Wilson estimate: 8.7 Å2 / Rmerge(I) obs: 0.059 |
Reflection shell | Resolution: 2→2.03 Å / Rmerge(I) obs: 0.185 / Num. unique all: 1039 / % possible all: 95.8 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. measured all: 122607 |
Reflection shell | *PLUS % possible obs: 95.8 % |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 6atj Resolution: 2→20 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 357352.24 / Data cutoff high rms absF: 357352.24 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: PDB entry 6atj without water was used as a starting model.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 55.9162 Å2 / ksol: 0.379372 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.04 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 19
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Xplor file |
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Refinement | *PLUS Lowest resolution: 20 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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