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- PDB-1iqc: Crystal structure of Di-Heme Peroxidase from Nitrosomonas europaea -
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Open data
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Basic information
Entry | Database: PDB / ID: 1iqc | |||||||||
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Title | Crystal structure of Di-Heme Peroxidase from Nitrosomonas europaea | |||||||||
![]() | di-heme peroxidase | |||||||||
![]() | OXIDOREDUCTASE / Di-Heme Peroxidase / Nitrosomonas europaea / Proteobacteria / beta subdivision / Ammonia-oxidizing bacteria | |||||||||
Function / homology | ![]() cytochrome-c peroxidase / cytochrome-c peroxidase activity / periplasmic space / electron transfer activity / heme binding / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Shimizu, H. | |||||||||
![]() | ![]() Title: Crystal structure of Nitrosomonas europaea cytochrome c peroxidase and the structural basis for ligand switching in bacterial di-heme peroxidases Authors: Shimizu, H. / Schuller, D.J. / Lanzilotta, W.N. / Sundaramoorthy, M. / Arciero, D.M. / Hooper, A.B. / Poulos, T.L. #1: ![]() Title: Crystallization and Preliminary Crystallographic Analysis of Cytochrome C553 Peroxidase from Nitrosomonas europaea Authors: Pappa, H. / Li, H. / Sundaramoorthy, M. / Arciero, D. / Hooper, A. / Poulos, T.L. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 275.9 KB | Display | ![]() |
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PDB format | ![]() | 222.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 942.4 KB | Display | ![]() |
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Full document | ![]() | 978.8 KB | Display | |
Data in XML | ![]() | 30.3 KB | Display | |
Data in CIF | ![]() | 47.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 34019.191 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Non-polymers , 5 types, 874 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HEC.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HEC.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-CA / #3: Chemical | #4: Chemical | ChemComp-HEC / #5: Chemical | ChemComp-GOL / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.73 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG8000, MgCl2, Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Details: Pappa, H., (1996) J.STRUCT.BIOL., 116, 429. | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 15, 2000 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. all: 393924 / Num. obs: 119903 / % possible obs: 96 % / Observed criterion σ(F): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 23.2 Å2 / Rmerge(I) obs: 0.031 / Net I/σ(I): 13 |
Reflection shell | Resolution: 1.8→1.91 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.1 / Mean I/σ(I) obs: 5.3 / Num. unique all: 14974 / % possible all: 89.1 |
Reflection | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 30 Å / % possible obs: 96 % / Num. measured all: 393924 |
Reflection shell | *PLUS % possible obs: 89.1 % / Rmerge(I) obs: 0.13 |
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Processing
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Refinement | Method to determine structure: ![]()
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Refinement step | Cycle: LAST / Resolution: 1.8→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.91 Å / Rfactor Rfree error: 0.01
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Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 50 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.222 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 1.9 Å / Rfactor Rfree: 0.306 / Rfactor Rwork: 0.257 |