+Open data
-Basic information
Entry | Database: PDB / ID: 1h57 | ||||||
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Title | Structure of horseradish peroxidase C1A compound III | ||||||
Components | PEROXIDASE C1A | ||||||
Keywords | OXIDOREDUCTASE / PEROXIDASE / HORSERADISH / CATALYTIC INTERMEDIATE / COMPOUND III / OXYPEROXIDASE | ||||||
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 / OTHER / Resolution: 1.6 Å | ||||||
Authors | Berglund, G.I. / Carlsson, G.H. / Hajdu, J. | ||||||
Citation | Journal: Nature / Year: 2002 Title: The Catalytic Pathway of Horseradish Peroxidase at High Resolution Authors: Berglund, G.I. / Carlsson, G.H. / Smith, A.T. / Szoke, H. / Henriksen, A. / Hajdu, J. #1: 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. #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. #3: Journal: J.Biol.Chem. / Year: 1990 Title: Expression of a Synthetic Gene for Horseradish Peroxidase C in Escherichia Coli and Folding and Activation of the Recombinant Enzyme with Ca2+ and Heme Authors: Smith, A.T. / Santama, N. / Dacey, S. / Edwards, M. / Bray, R.C. / Thorneley, R.N. / 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 | 1h57.cif.gz | 82 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1h57.ent.gz | 64.9 KB | Display | PDB format |
PDBx/mmJSON format | 1h57.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h5/1h57 ftp://data.pdbj.org/pub/pdb/validation_reports/h5/1h57 | HTTPS FTP |
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-Related structure data
Related structure data | 1h55C 1h58C 1h5aC 1h5cC 1h5dC 1h5eC 1h5fC 1h5gC 1h5hC 1h5iC 1h5jC 1h5kC 1h5lC 1h5mC 1hchC 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 33948.141 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ARMORACIA RUSTICANA (horseradish) / Description: SYNTHETIC GENE / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P00433, peroxidase |
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-Non-polymers , 6 types, 410 molecules
#2: Chemical | ChemComp-HEM / | ||||||
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#3: Chemical | ChemComp-ACT / | ||||||
#4: Chemical | #5: Chemical | ChemComp-OXY / | #6: Chemical | #7: Water | ChemComp-HOH / | |
-Details
Sequence details | THE SWS ENTRY INCLUDES N-TERM AND C-TERM SIGNAL PEPTIDES. |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 17 |
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-Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.1 % Description: DATA WAS ALSO COLLECTED AT BM14 (0.850 A) AND ID14-EH3 (0.936 A) AT THE ESRF (SEE JRNL) STARTING MODEL FOR RIGID-BODY REFINEMENT WAS PDB ENTRY 7ATJ |
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Crystal grow | pH: 6.5 Details: 20% (W/V) PEG 4000 0.2 M CALCIUM ACETATE, 0.1 M CACODYLATE BUFFER, PH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.827 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 15, 1999 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.827 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→33.2 Å / Num. obs: 40949 / % possible obs: 95.5 % / Redundancy: 4.05 % / Biso Wilson estimate: 15.7 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 1.6→1.64 Å / Rmerge(I) obs: 0.389 / Mean I/σ(I) obs: 3.5 / % possible all: 93.7 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER / Resolution: 1.6→33.18 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1400728.89 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: SER 306 WAS THE LAST RESIDUE SEEN IN THE ELECTRON DENSITY MAP THE FOLLOWING RESIDUES HAVE BEEN MODELLED IN MULTIPLE CONFORMATIONS: 15,91,151,161,188,219,240, 249,264,503
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 48.8241 Å2 / ksol: 0.352013 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→33.18 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.7 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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Xplor file |
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