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- PDB-4cvy: Crystal structure of the M. tuberculosis sulfate ester dioxygenas... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4cvy | ||||||
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Title | Crystal structure of the M. tuberculosis sulfate ester dioxygenase Rv3406 in complex with iron. | ||||||
![]() | DIOXYGENASE RV3406/MT3514 | ||||||
![]() | OXIDOREDUCTASE / DRUG DESIGN / DIOXYGENASE / DPRE1 / MYCOBACTERIAL ENZYMES | ||||||
Function / homology | ![]() alkyl sulfatase / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor / 2-oxoglutarate-dependent dioxygenase activity / dioxygenase activity / response to antibiotic / metal ion binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Neres, J. / Hartkoorn, R.C. / Chiarelli, L.R. / Gadupudi, R. / Pasca, M. / Mori, G. / Farina, D. / Salina, S. / Makarov, V. / Kolly, G.S. ...Neres, J. / Hartkoorn, R.C. / Chiarelli, L.R. / Gadupudi, R. / Pasca, M. / Mori, G. / Farina, D. / Salina, S. / Makarov, V. / Kolly, G.S. / Molteni, E. / Binda, C. / Dhar, N. / Ferrari, S. / Brodin, P. / Delorme, V. / Landry, V. / de Jesus Lopes Ribeiro, A.L. / Saxena, P. / Pojer, F. / Venturelli, A. / Carta, A. / Luciani, R. / Porta, A. / Zanoni, G. / De Rossi, E. / Costi, M.P. / Riccardi, G. / Cole, S.T. | ||||||
![]() | ![]() Title: 2-Carboxyquinoxalines Kill Mycobacterium Tuberculosis Through Noncovalent Inhibition of Dpre1. Authors: Neres, J. / Hartkoorn, R.C. / Chiarelli, L.R. / Gadupudi, R. / Pasca, M.R. / Mori, G. / Venturelli, A. / Savina, S. / Makarov, V. / Kolly, G.S. / Molteni, E. / Binda, C. / Dhar, N. / ...Authors: Neres, J. / Hartkoorn, R.C. / Chiarelli, L.R. / Gadupudi, R. / Pasca, M.R. / Mori, G. / Venturelli, A. / Savina, S. / Makarov, V. / Kolly, G.S. / Molteni, E. / Binda, C. / Dhar, N. / Ferrari, S. / Brodin, P. / Delorme, V. / Landry, V. / De Jesus Lopes Ribeiro, A.L. / Farina, D. / Saxena, P. / Pojer, F. / Carta, A. / Luciani, R. / Porta, A. / Zanoni, G. / De Rossi, E. / Costi, M.P. / Riccardi, G. / Cole, S.T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 200 KB | Display | ![]() |
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PDB format | ![]() | 158.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 474.4 KB | Display | ![]() |
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Full document | ![]() | 486.4 KB | Display | |
Data in XML | ![]() | 36 KB | Display | |
Data in CIF | ![]() | 50.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4p8cC ![]() 4p8kC ![]() 4p8lC ![]() 4p8mC ![]() 4p8nC ![]() 4p8pC ![]() 4p8tC ![]() 4p8yC ![]() 4ffaS 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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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 32618.855 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P65075, UniProt: P9WKZ1*PLUS, Oxidoreductases #2: Chemical | ChemComp-NO3 / | #3: Chemical | ChemComp-FE / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 44 % / Description: NONE |
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Crystal grow | Details: 22% PEG2000, 300 MM MAGNESIUM NITRATE, 100 MM TRIS/HCL PH 8.0, 2% MPD |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PILATUS / Detector: PIXEL / Date: Sep 11, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2→43.4 Å / Num. obs: 74877 / % possible obs: 98 % / Observed criterion σ(I): 2 / Redundancy: 4.7 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 2→2.04 Å |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4FFA Resolution: 2→94.04 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.931 / SU B: 6.769 / SU ML: 0.174 / Cross valid method: THROUGHOUT / ESU R: 0.185 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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: 39.837 Å2
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Refinement step | Cycle: LAST / Resolution: 2→94.04 Å
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Refine LS restraints |
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