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Yorodumi- PDB-4atj: DISTAL HEME POCKET MUTANT (H42E) OF RECOMBINANT HORSERADISH PEROX... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4atj | ||||||
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Title | DISTAL HEME POCKET MUTANT (H42E) OF RECOMBINANT HORSERADISH PEROXIDASE IN COMPLEX WITH BENZHYDROXAMIC ACID | ||||||
Components | PROTEIN (PEROXIDASE C1A) | ||||||
Keywords | OXIDOREDUCTASE / PEROXIDASE / 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 / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Meno, K. / Jennings, S. / Smith, A.T. / Henriksen, A. / 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: 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. #2: 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4atj.cif.gz | 141.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4atj.ent.gz | 109.2 KB | Display | PDB format |
PDBx/mmJSON format | 4atj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/at/4atj ftp://data.pdbj.org/pub/pdb/validation_reports/at/4atj | HTTPS FTP |
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-Related structure data
Related structure data | 1kzmC 2atjS 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-1, -0.0063, 0.0026), Vector: |
-Components
#1: Protein | Mass: 34070.309 Da / Num. of mol.: 2 / Mutation: H42E Source method: isolated from a genetically manipulated source Details: CONTAINS HEME, TWO STRUCTURAL CALCIUM IONS, AND BENZHYDROXAMIC ACID BOUND IN ACTIVE SITE Source: (gene. exp.) Armoracia rusticana (horseradish) / Production host: Escherichia coli (E. coli) / References: UniProt: P00433, peroxidase #2: Chemical | ChemComp-CA / #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Nonpolymer details | THE CHARGE IS UNKNOWN SINCE IT IS POSITIONED IN THE ACTIVE SITE, WHICH CHANGES THE NORMAL PKA. THE ...THE CHARGE IS UNKNOWN SINCE IT IS POSITIONED | Sequence details | THE N-TERMINAL METHIONINE ORIGINATES FROM THE E. COLI EXPRESSION SYSTEM. RESIDUES 1 - 29 AND 339 - ...THE N-TERMINAL METHIONINE | |
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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: 2.6 Å3/Da / Density % sol: 52.7 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 / Details: pH 6.5 | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 283 K / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 290 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Jul 1, 1997 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→45 Å / Num. obs: 23291 / % possible obs: 93.2 % / Observed criterion σ(I): -3 / Redundancy: 2.6 % / Biso Wilson estimate: 11.4 Å2 / Rmerge(I) obs: 0.132 / Net I/σ(I): 7 |
Reflection shell | Resolution: 2.5→2.54 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 3 / % possible all: 95.4 |
Reflection | *PLUS Lowest resolution: 45 Å / Num. obs: 23302 / % possible obs: 95.4 % / Redundancy: 3.4 % / Num. measured all: 79639 |
Reflection shell | *PLUS % possible obs: 95.4 % / Rmerge(I) obs: 0.39 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2ATJ Resolution: 2.5→45 Å / Rfactor Rfree error: 0.004 / 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. THE STRUCTURE WAS REFINED USING STRICT NON- CRYSTALLOGRAPHIC SYMMETRY CONSTRAINTS.
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Displacement parameters | Biso mean: 17.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→45 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTRAINTS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.5→2.54 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 20
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 45 Å / Rfactor Rfree: 0.192 / Rfactor Rwork: 0.161 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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