[English] 日本語
Yorodumi- PDB-2c82: X-Ray Structure Of 1-Deoxy-D-xylulose 5-phosphate Reductoisomeras... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2c82 | ||||||
---|---|---|---|---|---|---|---|
Title | X-Ray Structure Of 1-Deoxy-D-xylulose 5-phosphate Reductoisomerase, DXR, Rv2870c, From Mycobacterium tuberculosis | ||||||
Components | 1-DEOXY-D-XYLULOSE 5-PHOSPHATE REDUCTOISOMERASE | ||||||
Keywords | OXIDOREDUCTASE / 1-DEOXY-D-XYLULOSE 5-PHOSPHATE REDUCTOISOMERASE / RV2870C / DOXP/MEP PATHWAY / ISOPRENE BIOSYNTHESIS / METAL-BINDING / NADP | ||||||
Function / homology | Function and homology information terpenoid biosynthetic process, mevalonate-independent / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway involved in terpenoid biosynthetic process / 1-deoxy-D-xylulose-5-phosphate reductoisomerase / 1-deoxy-D-xylulose-5-phosphate reductoisomerase activity / cobalt ion binding / NADPH binding / manganese ion binding / magnesium ion binding Similarity search - Function | ||||||
Biological species | MYCOBACTERIUM TUBERCULOSIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Henriksson, L.M. / Bjorkelid, C. / Mowbray, S.L. / Unge, T. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2006 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. | ||||||
History |
| ||||||
Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. | ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2c82.cif.gz | 155.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2c82.ent.gz | 122 KB | Display | PDB format |
PDBx/mmJSON format | 2c82.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2c82_validation.pdf.gz | 452.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2c82_full_validation.pdf.gz | 456.9 KB | Display | |
Data in XML | 2c82_validation.xml.gz | 29.7 KB | Display | |
Data in CIF | 2c82_validation.cif.gz | 43.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c8/2c82 ftp://data.pdbj.org/pub/pdb/validation_reports/c8/2c82 | HTTPS FTP |
-Related structure data
Related structure data | 1q0qS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||
Unit cell |
| ||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: MET / End label comp-ID: MET / Refine code: 1 / Auth seq-ID: 11 - 389 / Label seq-ID: 11 - 389
NCS oper: (Code: given Matrix: (-1, -0.001, 0.0002), Vector: |
-Components
#1: Protein | Mass: 42896.344 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Plasmid: PET101D-TOPO / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P64012, UniProt: P9WNS1*PLUS, 1-deoxy-D-xylulose-5-phosphate reductoisomerase #2: Chemical | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46 % |
---|---|
Crystal grow | Method: vapor diffusion, sitting drop Details: THE SITTING DROPS CONTAINED 1 ML PROTEIN, 5.35 MG/ML, WITH A FINAL CONCENTRATION OF 0.64 MM OF FOSMIDOMYCIN, DISSOLVED IN 10 MM TRIS PH 8.0, AND 1 ML CRYSTALLIZATION BUFFER (40% ETHYLENE ...Details: THE SITTING DROPS CONTAINED 1 ML PROTEIN, 5.35 MG/ML, WITH A FINAL CONCENTRATION OF 0.64 MM OF FOSMIDOMYCIN, DISSOLVED IN 10 MM TRIS PH 8.0, AND 1 ML CRYSTALLIZATION BUFFER (40% ETHYLENE GLYCOL, 2 MM MGSO4, 20 MM DTT, 0.2 MM EDTA, AND 100 MM ACETATE PH 5.0). THE RESERVOIR SOLUTION CONSISTED OF A MIXTURE BETWEEN THE CRYSTALLIZATION BUFFER, AND THE BUFFER USED IN THE FINAL STEPS OF THE PROTEIN PURIFICATION (75 MM NACL, 10 MM TRIS-HCL PH 7.5, 20% ETHYLENE GLYCOL, 1 MM MGSO4, 10 MM DTT, 0.1 MM EDTA, AND 50 MM ACETATE PH 5.0). BEFORE THE CRYSTALS WERE FLASH-COOLED IN LIQUID NITROGEN THEY WERE TRANSFERRED TO A DROP WITH THE RESERVOIR SOLUTION COMPLEMENTED WITH AN ADDITIONAL 10% ETHYLENE GLYCOL, AND 1 MM FOSMIDOMYCIN. |
-Data collection
Diffraction | Mean temperature: 110 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 1.072 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 17, 2005 |
Radiation | Monochromator: SILICON (111) CHANNEL-CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.072 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→40 Å / Num. obs: 56321 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 6.2 |
Reflection shell | Resolution: 1.9→1.95 Å / Rmerge(I) obs: 0.39 / % possible all: 99.8 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1Q0Q Resolution: 1.9→40 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.932 / SU B: 3.946 / SU ML: 0.118 / Cross valid method: THROUGHOUT / ESU R: 0.177 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.13 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→40 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|