+Open data
-Basic information
Entry | Database: PDB / ID: 1w4w | ||||||
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Title | Ferric horseradish peroxidase C1A in complex with formate | ||||||
Components | HORSERADISH PEROXIDASE C1A | ||||||
Keywords | OXIDOREDUCTASE / FORMATE ION / CALCIUM / FERRIC STATE / GLYCOPROTEIN / HEME / HORSERADISH / IRON / MULTIGENE FAMILY / PEROXIDASE / PYRROLIDONE CARBOXYLIC ACID | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Carlsson, G.H. / Nicholls, P. / Svistunenko, D. / Berglund, G.I. / Hajdu, J. | ||||||
Citation | Journal: Biochemistry / Year: 2005 Title: Complexes of Horseradish Peroxidase with Formate, Acetate, and Carbon Monoxide Authors: Carlsson, G.H. / Nicholls, P. / Svistunenko, D. / Berglund, G.I. / Hajdu, J. #1: 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. #2: 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 | 1w4w.cif.gz | 86.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1w4w.ent.gz | 62.1 KB | Display | PDB format |
PDBx/mmJSON format | 1w4w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w4/1w4w ftp://data.pdbj.org/pub/pdb/validation_reports/w4/1w4w | HTTPS FTP |
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-Related structure data
Related structure data | 1w4yC 1h5aS 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: 35652.125 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: A FORMATE ION IS BOUND IN THE ACTIVE SITE / Source: (gene. exp.) ARMORACIA RUSTICANA (horseradish) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P00433, peroxidase | ||||
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#2: Chemical | ChemComp-HEM / | ||||
#3: Chemical | #4: Chemical | ChemComp-FMT / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 7 |
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-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.6 % Description: DATA COLLECTED USING A MULTICRYSTAL STRATEGY TO DECREASE THE X-RAY INDUCED REDUCTION OF THE IRON |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 20% PEG8000, 0.2M CA-ACETATE, 0.1 M NA-CACODYLATE PH 6.5, FERULIC ACID AS ADDITIVE STREAK SEEDING, HANGING DROP, 4DEGC |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.089 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 26, 2003 / Details: SI(III) |
Radiation | Monochromator: MULTIPOLE WIGGLER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.089 Å / Relative weight: 1 |
Reflection | Resolution: 1.51→50 Å / Num. obs: 49541 / % possible obs: 96 % / Observed criterion σ(I): 3 / Redundancy: 3.7 % / Biso Wilson estimate: 17.7 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 1.51→1.57 Å / Rmerge(I) obs: 0.24 / % possible all: 78.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1H5A Resolution: 1.55→29.87 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1343934.32 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 40.5205 Å2 / ksol: 0.32652 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.55→29.87 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.65 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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