+Open data
-Basic information
Entry | Database: PDB / ID: 3qdl | ||||||
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Title | Crystal structure of RdxA from Helicobacter pyroli | ||||||
Components | Oxygen-insensitive NADPH nitroreductase | ||||||
Keywords | OXIDOREDUCTASE / oxygen-insensitive NAD(P)H nitroreductase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Helicobacter pylori (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å | ||||||
Authors | Rojas, A.L. / Martinez-Julvez, M. / Olekhnovich, I.N. / Hoffman, P.S. / Sancho, J. | ||||||
Citation | Journal: Febs J. / Year: 2012 Title: Structure of RdxA--an oxygen-insensitive nitroreductase essential for metronidazole activation in Helicobacter pylori. Authors: Martinez-Julvez, M. / Rojas, A.L. / Olekhnovich, I. / Espinosa Angarica, V. / Hoffman, P.S. / Sancho, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3qdl.cif.gz | 152.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qdl.ent.gz | 118.9 KB | Display | PDB format |
PDBx/mmJSON format | 3qdl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qd/3qdl ftp://data.pdbj.org/pub/pdb/validation_reports/qd/3qdl | HTTPS FTP |
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-Related structure data
Related structure data | 1icrS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 24101.039 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: rdxA, HP_0954 / Plasmid: pET15brdxA5 / Production host: Escherichia coli (E. coli) / References: UniProt: O25608 #2: Chemical | ChemComp-FMN / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 1.93 Å3/Da / Density % sol: 36.27 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 25 % PEG 3350, 0.1 M Bis-Tris, 0.2 M MgCl2, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Redundancy: 5.5 % / Av σ(I) over netI: 3.6 / Number: 266704 / Rsym value: 0.145 / D res high: 2 Å / D res low: 76.12 Å / Num. obs: 48813 / % possible obs: 99.7 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection twin |
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Reflection | Resolution: 2→76.12 Å / Num. all: 48813 / Num. obs: 48813 / % possible obs: 99.7 % / Redundancy: 5.5 % / Rsym value: 0.145 / Net I/σ(I): 8.1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1,2
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Rfactor: 53 / 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 1icr Resolution: 2→76.12 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.91 / WRfactor Rfree: 0.2337 / WRfactor Rwork: 0.1992 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8542 / SU B: 2.964 / SU ML: 0.083 / SU R Cruickshank DPI: 0.0403 / SU Rfree: 0.0335 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.033 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 49.8 Å2 / Biso mean: 19.935 Å2 / Biso min: 2 Å2
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Refinement step | Cycle: LAST / Resolution: 2→76.12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.999→2.051 Å / Total num. of bins used: 20
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