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- PDB-2jd0: X-ray structure of mutant 1-deoxy-D-xylulose 5-phosphate reductoi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2jd0 | ||||||
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Title | X-ray structure of mutant 1-deoxy-D-xylulose 5-phosphate reductoisomerase, DXR, Rv2870c, from Mycobacterium tuberculosis, in complex with NADPH | ||||||
![]() | 1-DEOXY-D-XYLULOSE 5-PHOSPHATE REDUCTOISOMERASE | ||||||
![]() | OXIDOREDUCTASE / DOXP/MEP PATHWAY / ISOPRENE BIOSYNTHESIS / 1-DEOXY-D-XYLULOSE 5-PHOSPHATE REDUCTOISOMERASE / NADP / RV2870C / METAL-BINDING | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Henriksson, L.M. / Unge, T. / Jones, T.A. / Mowbray, S.L. | ||||||
![]() | ![]() 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 |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. | ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 156 KB | Display | ![]() |
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PDB format | ![]() | 121.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 744 KB | Display | ![]() |
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Full document | ![]() | 753.7 KB | Display | |
Data in XML | ![]() | 30.2 KB | Display | |
Data in CIF | ![]() | 43.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2jcvC ![]() 2jcxC ![]() 2jcyC ![]() 2jd1C ![]() 2jd2C ![]() 4aicC ![]() 2c82S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.4991, 0.8531, 0.1523), Vector: |
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Components
#1: Protein | Mass: 41699.000 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-389 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P64012, UniProt: P9WNS1*PLUS, 1-deoxy-D-xylulose-5-phosphate reductoisomerase #2: Chemical | ChemComp-NDP / | #3: Chemical | #4: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, ASP 151 TO ASN ENGINEERED RESIDUE IN CHAIN A, GLU 222 TO GLN ...ENGINEERED | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.5 % |
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Oct 5, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→35 Å / Num. obs: 32964 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 2.3→2.36 Å / Rmerge(I) obs: 0.43 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2C82 Resolution: 2.3→35 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.891 / SU B: 7.694 / SU ML: 0.19 / Cross valid method: THROUGHOUT / ESU R: 0.406 / ESU R Free: 0.259 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THIS ENTRY CONTAINS ATOMS WITH REFINED B- FACTORS AND ZERO OCCUPANCY.
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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: 26.72 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→35 Å
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Refine LS restraints |
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