[English] 日本語
Yorodumi- PDB-1knc: Structure of AhpD from Mycobacterium tuberculosis, a novel enzyme... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1knc | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of AhpD from Mycobacterium tuberculosis, a novel enzyme with thioredoxin-like activity. | ||||||
Components | AhpD protein | ||||||
Keywords | ELECTRON TRANSPORT / AhpD / thioredoxin / disulfide / peroxiredoxin / lpd / redox | ||||||
Function / homology | Function and homology information lipoyl-dependent peroxiredoxin / hydroperoxide reductase activity / alkyl hydroperoxide reductase activity / Cell redox homeostasis / disulfide oxidoreductase activity / peroxiredoxin activity / cell redox homeostasis / peroxidase activity / response to oxidative stress / oxidoreductase activity ...lipoyl-dependent peroxiredoxin / hydroperoxide reductase activity / alkyl hydroperoxide reductase activity / Cell redox homeostasis / disulfide oxidoreductase activity / peroxiredoxin activity / cell redox homeostasis / peroxidase activity / response to oxidative stress / oxidoreductase activity / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2 Å | ||||||
Authors | Bryk, R. / Lima, C.D. / Erdjument-Bromage, H. / Tempst, P. / Nathan, C. | ||||||
Citation | Journal: Science / Year: 2002 Title: Metabolic enzymes of mycobacteria linked to antioxidant defense by a thioredoxin-like protein. Authors: Bryk, R. / Lima, C.D. / Erdjument-Bromage, H. / Tempst, P. / Nathan, C. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1knc.cif.gz | 114.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1knc.ent.gz | 90.8 KB | Display | PDB format |
PDBx/mmJSON format | 1knc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kn/1knc ftp://data.pdbj.org/pub/pdb/validation_reports/kn/1knc | HTTPS FTP |
---|
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
| ||||||||
Details | The AhpD trimer is composed of chains A, B, and C One trimer exists in the ASU |
-Components
#1: Protein | Mass: 18801.520 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P0A5N4, UniProt: P9WQB5*PLUS #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.51 Å3/Da / Density % sol: 64.91 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1.5-2.5M AmSO4, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
Crystal grow | *PLUS Method: vapor diffusion, hanging drop |
Components of the solutions | *PLUS Conc.: 1.5-2.5 M / Common name: ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9787 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 1, 2001 |
Radiation | Monochromator: sag focus / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9787 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. all: 55072 / Num. obs: 55072 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 23.1 Å2 / Rsym value: 0.077 / Net I/σ(I): 18 |
Reflection shell | Resolution: 2→2.07 Å / Mean I/σ(I) obs: 2.7 / Num. unique all: 5333 / Rsym value: 0.313 / % possible all: 98.9 |
Reflection | *PLUS Highest resolution: 2 Å / Num. measured all: 1515540 / Rmerge(I) obs: 0.077 |
Reflection shell | *PLUS % possible obs: 98.9 % / Rmerge(I) obs: 0.313 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MIR / Resolution: 2→20 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 3209216.61 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 56.4947 Å2 / ksol: 0.353314 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.1 Å2
| |||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→20 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
| |||||||||||||||||||||||||
Xplor file |
| |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor obs: 0.216 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 39.1 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
| |||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.309 / % reflection Rfree: 5.3 % / Rfactor Rwork: 0.304 |