[English] 日本語
![](img/lk-miru.gif)
- PDB-1kyq: Met8p: A bifunctional NAD-dependent dehydrogenase and ferrochelat... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1kyq | ||||||
---|---|---|---|---|---|---|---|
Title | Met8p: A bifunctional NAD-dependent dehydrogenase and ferrochelatase involved in siroheme synthesis. | ||||||
![]() | Siroheme biosynthesis protein MET8 | ||||||
![]() | OXIDOREDUCTASE / LYASE / homodimer | ||||||
Function / homology | ![]() precorrin-2 dehydrogenase / precorrin-2 dehydrogenase activity / sirohydrochlorin ferrochelatase / sirohydrochlorin ferrochelatase activity / siroheme biosynthetic process / ferrochelatase activity / sulfate assimilation / methionine biosynthetic process Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Schubert, H.L. / Raux, E. / Brindley, A.A. / Wilson, K.S. / Hill, C.P. / Warren, M.J. | ||||||
![]() | ![]() Title: The structure of Saccharomyces cerevisiae Met8p, a bifunctional dehydrogenase and ferrochelatase. Authors: Schubert, H.L. / Raux, E. / Brindley, A.A. / Leech, H.K. / Wilson, K.S. / Hill, C.P. / Warren, M.J. #1: ![]() Title: The Role of Saccharomyces cerevisiae Met1p and Met8p in Sirohaem and Cobalamin Biosynthesis Authors: Raux, E. / McVeigh, T. / Peters, S.E. / Leustek, T. / Warren, M.J. | ||||||
History |
| ||||||
Remark 999 | SEQUENCE During several rounds of independent PCR and sequencing from S. cervisiae, the authors ...SEQUENCE During several rounds of independent PCR and sequencing from S. cervisiae, the authors discovered several discrepancies in the primary sequence: K15R, I33(MSE) (a helpful mutation for solving the structure), E61K, D102N. |
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 186.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 155 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Similar structure data |
---|
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 32289.268 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: Met8 / Plasmid: pET14b / Production host: ![]() ![]() References: UniProt: P15807, Oxidoreductases, protoporphyrin ferrochelatase #2: Chemical | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.89 Å3/Da / Density % sol: 57.46 % | |||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG 4000, CaCl2, Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 60 % | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 30, 2001 / Details: Flat mirror (vertical focusing) |
Radiation | Monochromator: single crystal Si(311) bent monochromator (horizontal focusing) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. all: 64205 / Num. obs: 64205 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.1 % / Biso Wilson estimate: 28 Å2 / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Net I/σ(I): 15.7 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.304 / Mean I/σ(I) obs: 2.9 / Num. unique all: 9417 / Rsym value: 0.304 / % possible all: 100 |
Reflection | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 20 Å / Num. obs: 56148 / % possible obs: 98 % / Num. measured all: 117894 / Rmerge(I) obs: 0.07 |
Reflection shell | *PLUS % possible obs: 85.6 % / Rmerge(I) obs: 0.304 / Mean I/σ(I) obs: 3 |
-
Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Details: REFMAC MKLF. PORTIONS OF THE NAD LIGANDS WERE MISSING IN THE DENSITY.
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→30 Å
| ||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 5 % / Rfactor all: 0.22 / Rfactor obs: 0.221 / Rfactor Rfree: 0.287 / Rfactor Rwork: 0.221 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
|