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Open data
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Basic information
Entry | Database: PDB / ID: 1f8w | ||||||
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Title | CRYSTAL STRUCTURE OF NADH PEROXIDASE MUTANT: R303M | ||||||
![]() | NADH PEROXIDASE | ||||||
![]() | OXIDOREDUCTASE / Interface / FAD / NAD-binding domains | ||||||
Function / homology | ![]() NADH peroxidase / NADH peroxidase activity / flavin adenine dinucleotide binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Yeh, J.I. / Claiborne, A. / Hol, W.G.J. | ||||||
![]() | ![]() Title: Analysis of the kinetic and redox properties of the NADH peroxidase R303M mutant: correlation with the crystal structure. Authors: Crane III, E.J. / Yeh, J.I. / Luba, J. / Claiborne, A. #1: ![]() Title: Structure of the Native Cysteine-sulfenic Acid Redox Center of Enterococcal NADH Peroxidase Refined at 2.8 A Resolution Authors: Yeh, J.I. / Claiborne, A. / Hol, W.G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 98.7 KB | Display | ![]() |
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PDB format | ![]() | 80.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 464.4 KB | Display | ![]() |
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Full document | ![]() | 470.6 KB | Display | |
Data in XML | ![]() | 10.8 KB | Display | |
Data in CIF | ![]() | 16.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Details | FUNCTIONAL MOLECULE IS A HOMOTETRAMER |
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Components
#1: Protein | Mass: 49593.230 Da / Num. of mol.: 1 / Mutation: ARG 303 TO MET 303 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-FAD / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da | |||||||||||||||||||||||||
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 2% PEG 400, 2.0 M (NH4)2SO4, 100 mM Na Hepes, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 296K | |||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 8, 1996 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→99 Å / Num. all: 42662 / Num. obs: 36615 / % possible obs: 85.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.4 % / Biso Wilson estimate: 10.2 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 9.5 |
Reflection shell | Highest resolution: 2.45 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.363 / Mean I/σ(I) obs: 2.6 / Rsym value: 0.39 / % possible all: 71.1 |
Reflection | *PLUS Num. measured all: 60231 / Rmerge(I) obs: 0.048 |
Reflection shell | *PLUS Lowest resolution: 2.56 Å / % possible obs: 70.9 % |
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Processing
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Refinement | Resolution: 2.45→50 Å / Cross valid method: X-PLOR FreeR / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Refine analyze | Luzzati sigma a obs: 0.26 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.45→50 Å
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Refine LS restraints |
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Software | *PLUS Name: ![]() | |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 50 Å / σ(F): 2 / % reflection Rfree: 5 % / Rfactor obs: 0.196 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 39.1 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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