[English] 日本語
Yorodumi- PDB-3hzn: Structure of the Salmonella typhimurium nfnB dihydropteridine red... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3hzn | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of the Salmonella typhimurium nfnB dihydropteridine reductase | ||||||
Components | Oxygen-insensitive NAD(P)H nitroreductase | ||||||
Keywords | OXIDOREDUCTASE / alpha and beta protein / 3 layer sandwich / FMN-dependent nitroreductase like / Flavoprotein / FMN / NAD / NADP / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID | ||||||
Function / homology | Function and homology information : / 2,4,6-trinitrotoluene catabolic process / Oxidoreductases / oxidoreductase activity / cytosol Similarity search - Function | ||||||
Biological species | Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å | ||||||
Authors | Anderson, S.M. / Wawrzak, Z. / Onopriyenko, O. / Skarina, T. / Anderson, W.F. / Savchenko, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: TO BE PUBLISHED Title: Structure of the Salmonella typhimurium nfnB dihydropteridine reductase Authors: Anderson, S.M. / Wawrzak, Z. / Onopriyenko, O. / Skarina, T. / Anderson, W.F. / Savchenko, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3hzn.cif.gz | 372.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3hzn.ent.gz | 320.8 KB | Display | PDB format |
PDBx/mmJSON format | 3hzn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3hzn_validation.pdf.gz | 592.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3hzn_full_validation.pdf.gz | 652 KB | Display | |
Data in XML | 3hzn_validation.xml.gz | 86.1 KB | Display | |
Data in CIF | 3hzn_validation.cif.gz | 112.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hz/3hzn ftp://data.pdbj.org/pub/pdb/validation_reports/hz/3hzn | HTTPS FTP |
-Related structure data
Similar structure data | |
---|---|
Other databases |
-Links
-Assembly
-Components
-Protein , 1 types, 8 molecules ABCDEFGH
#1: Protein | Mass: 24539.711 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) Strain: LT2 / Gene: nfnB, nfsI, STM0578 / Production host: Escherichia coli (E. coli) / References: UniProt: P15888, Oxidoreductases |
---|
-Non-polymers , 8 types, 900 molecules
#2: Chemical | ChemComp-TLA / #3: Chemical | ChemComp-SIN / #4: Chemical | ChemComp-MLI / #5: Chemical | ChemComp-CL / #6: Chemical | #7: Chemical | ChemComp-NA / #8: Chemical | #9: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 4.55 Å3/Da / Density % sol: 72.99 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 60% tacsimate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 110 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 6, 2008 / Details: beryllium lense |
Radiation | Monochromator: C(111) diamond Laue monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. all: 137152 / Num. obs: 136466 / % possible obs: 99.5 % / Observed criterion σ(F): 1.73 / Observed criterion σ(I): 3 / Redundancy: 7.2 % / Rmerge(I) obs: 0.124 / Χ2: 0.999 / Net I/σ(I): 13.722 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 3 / Num. unique all: 13315 / Χ2: 0.946 / % possible all: 97.5 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 2.4→30 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.929 / WRfactor Rfree: 0.22 / WRfactor Rwork: 0.179 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.851 / SU B: 5.804 / SU ML: 0.131 / SU R Cruickshank DPI: 0.203 / SU Rfree: 0.185 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.203 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: REFINED INDIVIDUALLY
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 116.75 Å2 / Biso mean: 37.624 Å2 / Biso min: 2 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→30 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.4→2.462 Å / Total num. of bins used: 20
|