[English] 日本語
![](img/lk-miru.gif)
- PDB-2y1e: X-ray structure of 1-deoxy-D-xylulose 5-phosphate reductoisomeras... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2y1e | ||||||
---|---|---|---|---|---|---|---|
Title | X-ray structure of 1-deoxy-D-xylulose 5-phosphate reductoisomerase, DXR, Rv2870c, from Mycobacterium tuberculosis, in complex with manganese. | ||||||
![]() | 1-DEOXY-D-XYLULOSE 5-PHOSPHATE REDUCTOISOMERASE | ||||||
![]() | OXIDOREDUCTASE / DOXP/MEP PATHWAY | ||||||
Function / homology | ![]() RNA polymerase sigma factor, region 2, helix turn helix motif / Rna Polymerase Sigma Factor; Chain: A / NAD(P)-binding Rossmann-like Domain / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Henriksson, L.M. / Larsson, A.M.S. / Bergfors, T. / Bjorkelid, C. / Unge, T. / Mowbray, S.L. / Jones, T.A. | ||||||
![]() | ![]() Title: Design, Synthesis and X-Ray Crystallographic Studies of Alpha-Aryl Substituted Fosmidomycin Analogues as Inhibitors of Mycobacterium Tuberculosis 1-Deoxy-D-Xylulose-5-Phosphate Reductoisomerase Authors: Andaloussi, M. / Henriksson, L.M. / Wieckowska, A. / Lindh, M. / Bjorkelid, C. / Larsson, A.M.S. / Iyer, H. / Srinivasa, B.R. / Bergfors, T. / Unge, T. / Mowbray, S.L. / Larhed, M. / Jones, T.A. / Karlen, A. #1: ![]() Title: The 1.9 A Resolution Structure of Mycobacterium Tuberculosis 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase, a Potential Drug Target. Authors: Henriksson, L.M. / Bjorkelid, C. / Mowbray, S.L. / Unge, T. #2: ![]() Title: Structures of Mycobacterium Tuberculosis 1-Deoxy-D-Xylulose-5-Phosphate Reductoisomerase Provide New Insights Into Catalysis. Authors: Henriksson, L.M. / Unge, T. / Carlsson, J. / Aqvist, J. / Mowbray, S.L. / Jones, T.A. | ||||||
History |
| ||||||
Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. | ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. |
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 162.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 126.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 456 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 459.8 KB | Display | |
Data in XML | ![]() | 32.1 KB | Display | |
Data in CIF | ![]() | 48.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2y1cC ![]() 2y1dC ![]() 2y1fC ![]() 2y1gC ![]() 2jcz C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.4959, 0.8552, 0.1507), Vector: |
-
Components
#1: Protein | Mass: 41700.973 Da / Num. of mol.: 2 / Fragment: RESIDUES 24-412 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: A2VLK3, 1-deoxy-D-xylulose-5-phosphate reductoisomerase #2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.5 % / Description: NONE |
---|
-Data collection
Diffraction | Mean temperature: 110 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 16, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→44 Å / Num. obs: 84235 / % possible obs: 96.5 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 1.65→1.74 Å / Rmerge(I) obs: 0.39 / % possible all: 80.1 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2JCZ ![]() 2jcz Resolution: 1.65→44 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.941 / SU B: 1.791 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES A198-204 HAVE NOT BEEN MODELLED OWING TO DISORDER.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.726 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→44 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|