[English] 日本語
![](img/lk-miru.gif)
- PDB-1aa4: SPECIFICITY OF LIGAND BINDING IN A BURIED POLAR CAVITY OF CYTOCHR... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1aa4 | ||||||
---|---|---|---|---|---|---|---|
Title | SPECIFICITY OF LIGAND BINDING IN A BURIED POLAR CAVITY OF CYTOCHROME C PEROXIDASE | ||||||
![]() | CYTOCHROME C PEROXIDASE | ||||||
![]() | OXIDOREDUCTASE / PEROXIDASE | ||||||
Function / homology | ![]() cytochrome-c peroxidase / cytochrome-c peroxidase activity / response to reactive oxygen species / hydrogen peroxide catabolic process / mitochondrial intermembrane space / peroxidase activity / cellular response to oxidative stress / mitochondrial matrix / heme binding / mitochondrion / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Musah, R.A. / Fitzgerald, M.M. / Mcree, D.E. / Goodin, D.B. | ||||||
![]() | ![]() Title: A ligand-gated, hinged loop rearrangement opens a channel to a buried artificial protein cavity. Authors: Fitzgerald, M.M. / Musah, R.A. / McRee, D.E. / Goodin, D.B. #1: ![]() Title: Small Molecule Binding to an Artificially Created Cavity at the Active Site of Cytochrome C Peroxidase Authors: Fitzgerald, M.M. / Churchill, M.J. / Mcree, D.E. / Goodin, D.B. #2: ![]() Title: The Asp-His-Fe Triad of Cytochrome C Peroxidase Controls the Reduction Potential, Electronic Structure, and Coupling of the Tryptophan Free Radical to the Heme Authors: Goodin, D.B. / Mcree, D.E. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 86.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 64.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 747 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 753.4 KB | Display | |
Data in XML | ![]() | 14.3 KB | Display | |
Data in CIF | ![]() | 19.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1aesC ![]() 1aetC ![]() 1aeuC ![]() 1cciC ![]() 1rycC ![]() 1ccaS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 33458.258 Da / Num. of mol.: 1 / Mutation: T1M, T2K, P3T, W191G Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Cell line: BL21 / Cellular location: MITOCHONDRIA / Gene: CCP / Organelle: MITOCHONDRIA / Plasmid: PT7CCP / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / Gene (production host): CCP(MKT) / Production host: ![]() ![]() |
---|---|
#2: Chemical | ChemComp-HEM / |
#3: Water | ChemComp-HOH / |
Sequence details | THIS CYTOCHROME C PEROXIDASE DIFFERS FROM 2CYP BY STRAIN-RELATED SUBSTITUTIONS OF THR 52 BY ILE AND ...THIS CYTOCHROME |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 61 % | |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 6 / Details: 20% MPD, 40 MM PHOSPHATE PH 6.0 | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, sitting drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 290 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: May 1, 1993 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Highest resolution: 2.1 Å / Num. obs: 19099 / % possible obs: 79 % / Observed criterion σ(I): 0 / Redundancy: 1.7 % / Biso Wilson estimate: 33.9 Å2 / Rmerge(I) obs: 0.056 / Rsym value: 0.102 / Net I/σ(I): 19 |
Reflection shell | Resolution: 2.09→2.23 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 2.8 / Rsym value: 0.31 / % possible all: 35 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1CCA Resolution: 2.1→7 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.5 / σ(F): 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→7 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.189 / Rfactor Rwork: 0.189 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|