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- PDB-4f2i: Crystal structure of glutaredoxin-like NrdH from Mycobacterium tu... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4f2i | ||||||
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Title | Crystal structure of glutaredoxin-like NrdH from Mycobacterium tuberculosis | ||||||
![]() | Glutaredoxin NrdH, putative | ||||||
![]() | ELECTRON TRANSPORT / THIOREDOXIN FOLD / NRDH / GLUTAREDOXIN / REDOX PROTEIN | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Phulera, S. / Mande, S.C. | ||||||
![]() | ![]() Title: The Crystal Structure of Mycobacterium tuberculosis NrdH at 0.87 A Suggests a Possible Mode of Its Activity. Authors: Phulera, S. / Mande, S.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 45.3 KB | Display | ![]() |
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PDB format | ![]() | 31.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4hs1C ![]() 4k8mC ![]() 1r7hS 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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Components on special symmetry positions |
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Components
#1: Protein | Mass: 9125.329 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.8 Å3/Da / Density % sol: 31.68 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 22% PEG 3350, 0.15M ammonium nitrate, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||
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Diffraction source | Source: ![]() | |||||||||||||||||||||
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 22, 2011 / Details: Bruker multilayer | |||||||||||||||||||||
Radiation | Monochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54179 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 1.67→35.34 Å / Num. all: 8023 / Num. obs: 8023 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 18.1 | |||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1R7H Resolution: 1.67→26.23 Å / SU ML: 0.27 / σ(F): 1.41 / Phase error: 17.52 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.47 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.584 Å2 / ksol: 0.363 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.67→26.23 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6
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