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Open data
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Basic information
Entry | Database: PDB / ID: 1h58 | ||||||
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Title | STRUCTURE OF FERROUS HORSERADISH PEROXIDASE C1A | ||||||
![]() | PEROXIDASE C1A | ||||||
![]() | OXIDOREDUCTASE / PEROXIDASE / HORSERADISH / FERROUS STATE | ||||||
Function / homology | ![]() lactoperoxidase activity / peroxidase / vacuole / hydrogen peroxide catabolic process / response to oxidative stress / heme binding / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Berglund, G.I. / Carlsson, G.H. / Hajdu, J. / Smith, A.T. / Szoke, H. / Henriksen, A. | ||||||
![]() | ![]() 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: ![]() 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: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 82.5 KB | Display | ![]() |
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PDB format | ![]() | 65.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 809.4 KB | Display | ![]() |
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Full document | ![]() | 810.3 KB | Display | |
Data in XML | ![]() | 17.7 KB | Display | |
Data in CIF | ![]() | 27.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1h55C ![]() 1h57C ![]() 1h5aC ![]() 1h5cC ![]() 1h5dC ![]() 1h5eC ![]() 1h5fC ![]() 1h5gC ![]() 1h5hC ![]() 1h5iC ![]() 1h5jC ![]() 1h5kC ![]() 1h5lC ![]() 1h5mC ![]() 1hchC C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 33948.141 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Chemical | ChemComp-HEM / | ||||
#3: Chemical | ChemComp-ACT / | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | THE SWS ENTRY INCLUDES N-TERM AND C-TERM SIGNAL PEPTIDES. | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.1 % Description: 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 THE FERROUS STATE WAS FORMED BY SOAKING THE CRYSTALS FOR 30 MINUTES IN A RESERVOIR SOLUTION SUPPLEMENTED WITH 100 ...Details: 20% (W/V) PEG 4000, 0.2 M CALCIUM ACETATE, 0.1 M CACODYLATE BUFFER, PH 6.5 THE FERROUS STATE WAS FORMED BY SOAKING THE CRYSTALS FOR 30 MINUTES IN A RESERVOIR SOLUTION SUPPLEMENTED WITH 100 MM SODIUM DITHIONITE AND PEG400 BEFORE FLASH FREEZING |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 15, 2000 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.983 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→25.9 Å / Num. obs: 34886 / % possible obs: 97.7 % / Redundancy: 3.4 % / Biso Wilson estimate: 13.1 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 16.7 |
Reflection shell | Resolution: 1.7→1.79 Å / Rmerge(I) obs: 0.156 / Mean I/σ(I) obs: 6.6 / % possible all: 97.7 |
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Processing
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Refinement | Method to determine structure: OTHER / Resolution: 1.7→25.9 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1391483.03 / 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 DUAL CONFORMATIONS: 15,16,24,73,91,151,161,176, 203,219,240,264 297,301,303
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 50.4185 Å2 / ksol: 0.378925 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→25.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.7 Å / Total num. of bins used: 6
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Xplor file |
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