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Yorodumi- PDB-2wqf: Crystal Structure of the Nitroreductase CinD from Lactococcus lac... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wqf | ||||||
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Title | Crystal Structure of the Nitroreductase CinD from Lactococcus lactis in Complex with FMN | ||||||
Components | COPPER INDUCED NITROREDUCTASE D | ||||||
Keywords | OXIDOREDUCTASE / NITROREDUCTASE / COPR REGULATED PROTEIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | LACTOCOCCUS LACTIS (lactic acid bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å | ||||||
Authors | Waltersperger, S.M. / Oberholzer, A.E. / Solioz, M. / Baumann, U. | ||||||
Citation | Journal: J.Bacteriol. / Year: 2010 Title: Structure and Function of Cind (Ytjd) of Lactococcus Lactis, a Copper-Induced Nitroreductase Involved in Defense Against Oxidative Stress. Authors: Mermod, M. / Mourlane, F. / Waltersperger, S. / Oberholzer, A.E. / Baumann, U. / Solioz, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wqf.cif.gz | 128.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wqf.ent.gz | 100.4 KB | Display | PDB format |
PDBx/mmJSON format | 2wqf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wq/2wqf ftp://data.pdbj.org/pub/pdb/validation_reports/wq/2wqf | HTTPS FTP |
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-Related structure data
Related structure data | 2ifaS S: Starting model for refinement |
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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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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 22562.412 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) LACTOCOCCUS LACTIS (lactic acid bacteria) Strain: IL1403 / Plasmid: PPROEX HTA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): DH5 ALPHA / References: UniProt: Q9CED0 |
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#2: Chemical | ChemComp-FMN / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.2 % / Description: NONE |
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Crystal grow | Details: 0.2M MGCL2, 0.1M TRISHCL PH 8.0, 5% MPD (V/V), 20% PEG 3350 (W/V), 1MM FMN, 4MM DTT |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→49.15 Å / Num. obs: 48865 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 8.9 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 12.36 |
Reflection shell | Resolution: 1.35→1.4 Å / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 1.9 / % possible all: 97.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2IFA Resolution: 1.35→32.134 Å / SU ML: 0 / σ(F): 2 / Phase error: 14.86 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 63.023 Å2 / ksol: 0.404 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.35→32.134 Å
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Refine LS restraints |
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LS refinement shell |
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