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Yorodumi- PDB-3r5p: Structure of Ddn, the Deazaflavin-dependent nitroreductase from M... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3r5p | ||||||
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Title | Structure of Ddn, the Deazaflavin-dependent nitroreductase from Mycobacterium tuberculosis involved in bioreductive activation of PA-824 | ||||||
Components | Deazaflavin-dependent nitroreductase | ||||||
Keywords | OXIDOREDUCTASE / PA-824 / split barrel-like fold / DUF385 / Deazaflavin-dependent nitroreductase / nitroimidazoles | ||||||
Function / homology | Function and homology information Oxidoreductases; Acting on the CH-OH group of donors; With other, known, physiological acceptors / coenzyme F420 binding / Oxidoreductases / peptidoglycan-based cell wall / oxidoreductase activity / plasma membrane Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å | ||||||
Authors | Cellitti, S.E. / Shaffer, J. / Jones, D.H. / Mukherjee, T. / Gurumurthy, M. / Bursulaya, B. / Boshoff, H.I.M. / Choi, I. / Nayya, A. / Lee, Y.S. ...Cellitti, S.E. / Shaffer, J. / Jones, D.H. / Mukherjee, T. / Gurumurthy, M. / Bursulaya, B. / Boshoff, H.I.M. / Choi, I. / Nayya, A. / Lee, Y.S. / Cherian, J. / Niyomrattanakit, P. / Dick, T. / Manjunatha, U.H. / Barry, C.E. / Spraggon, G. / Geierstanger, B.H. | ||||||
Citation | Journal: Structure / Year: 2012 Title: Structure of Ddn, the deazaflavin-dependent nitroreductase from Mycobacterium tuberculosis involved in bioreductive activation of PA-824. Authors: Cellitti, S.E. / Shaffer, J. / Jones, D.H. / Mukherjee, T. / Gurumurthy, M. / Bursulaya, B. / Boshoff, H.I. / Choi, I. / Nayyar, A. / Lee, Y.S. / Cherian, J. / Niyomrattanakit, P. / Dick, T. ...Authors: Cellitti, S.E. / Shaffer, J. / Jones, D.H. / Mukherjee, T. / Gurumurthy, M. / Bursulaya, B. / Boshoff, H.I. / Choi, I. / Nayyar, A. / Lee, Y.S. / Cherian, J. / Niyomrattanakit, P. / Dick, T. / Manjunatha, U.H. / Barry, C.E. / Spraggon, G. / Geierstanger, B.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3r5p.cif.gz | 40.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3r5p.ent.gz | 26.3 KB | Display | PDB format |
PDBx/mmJSON format | 3r5p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r5/3r5p ftp://data.pdbj.org/pub/pdb/validation_reports/r5/3r5p | HTTPS FTP |
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-Related structure data
Related structure data | 3r5lSC 3r5rC 3r5wC 3r5yC 3r5zC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | AUTHORS STATE THAT THE BIOLOGICAL ASSEMBLY IS UNKNOWN. |
-Components
#1: Protein | Mass: 13364.905 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: ddn, MT3651, Rv3547 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) References: UniProt: P71854, UniProt: P9WP15*PLUS, Oxidoreductases | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.37 Å3/Da / Density % sol: 63.47 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4 Details: 1.6M (NH4)2SO4, 0.1M Citric acid, pH 4.0, vapor diffusion, sitting drop, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.976 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 17, 2009 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 4.9 % / Av σ(I) over netI: 12.36 / Number: 82014 / Rmerge(I) obs: 0.116 / Χ2: 0.87 / D res high: 1.75 Å / D res low: 50 Å / Num. obs: 16598 / % possible obs: 90.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 1.85→50 Å / Num. all: 15215 / Num. obs: 15215 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Rmerge(I) obs: 0.113 / Χ2: 0.884 / Net I/σ(I): 12.4 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Rfactor: 46.66 / Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3R5L (preliminary model used for MR) Resolution: 1.85→41.645 Å / Occupancy max: 1 / Occupancy min: 0.44 / SU ML: 0.22 / σ(F): 0.16 / Phase error: 19.06 / Stereochemistry target values: CCP4 monomer library
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.477 Å2 / ksol: 0.393 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 82.33 Å2 / Biso mean: 24.6311 Å2 / Biso min: 9.01 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→41.645 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: 5
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