[English] 日本語
Yorodumi- PDB-8qes: E coli NfsB with the unnatural amino acid, p-aminoPhe at position 124 -
+Open data
-Basic information
Entry | Database: PDB / ID: 8qes | ||||||
---|---|---|---|---|---|---|---|
Title | E coli NfsB with the unnatural amino acid, p-aminoPhe at position 124 | ||||||
Components | Oxygen-insensitive NAD(P)H nitroreductase | ||||||
Keywords | OXIDOREDUCTASE / Nitroreductase / unnatural amino acid p-aminoPhenylalanine | ||||||
Function / homology | Function and homology information oxidoreductase activity, acting on other nitrogenous compounds as donors, with NAD or NADP as acceptor / 6,7-dihydropteridine reductase / 2,4,6-trinitrotoluene catabolic process / 6,7-dihydropteridine reductase activity / NAD(P)H dehydrogenase (quinone) activity / Oxidoreductases / FMN binding / protein homodimerization activity / identical protein binding / membrane / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 Å | ||||||
Authors | Day, M.A. / White, S.A. / Hyde, E.I. | ||||||
Funding support | United Kingdom, 1items
| ||||||
Citation | Journal: To Be Published Title: The structure of E coli NfsB nitroreducasr with unnatural amino acids at position 124 Authors: Day, M.A. / White, S.A. / Searle, P.F. / Hyde, E.I. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8qes.cif.gz | 188.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8qes.ent.gz | 149.2 KB | Display | PDB format |
PDBx/mmJSON format | 8qes.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8qes_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8qes_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 8qes_validation.xml.gz | 34.9 KB | Display | |
Data in CIF | 8qes_validation.cif.gz | 48.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qe/8qes ftp://data.pdbj.org/pub/pdb/validation_reports/qe/8qes | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 24423.623 Da / Num. of mol.: 4 / Mutation: F124(HOX) Source method: isolated from a genetically manipulated source Details: DRWGS remains from cleavage of tag in place of N-terminal Met. Residue 124 of NfsB replaced by p-aminoPhe (HOX) Source: (gene. exp.) Escherichia coli (E. coli) / Strain: DH5a / Gene: nfsB, dprA, nfnB, nfsI, ntr, b0578, JW0567 / Plasmid: pBAD_NTR_124TAG, pDule-pAF Details (production host): pBAD encodes NTR with stop codon at position 124; pDule contains a suppressor tRNA and an aminoacyl tRNAsynthetase Production host: Escherichia coli (E. coli) / Strain (production host): DH10B References: UniProt: P38489, Oxidoreductases, 6,7-dihydropteridine reductase #2: Chemical | ChemComp-FMN / #3: Chemical | ChemComp-NIO / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.72 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 100 mM Sodium acetate, pH 4.6, 15 mM nicotinic acid, 15% Ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 18, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.48→53.81 Å / Num. obs: 32949 / % possible obs: 99.6 % / Redundancy: 3.44 % / Biso Wilson estimate: 14.16 Å2 / Rsym value: 0.094 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 2.48→2.548 Å / Num. unique obs: 2264 / Rsym value: 0.26 / % possible all: 99.3 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.48→53.81 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.918 / SU B: 7.505 / SU ML: 0.167 / Cross valid method: THROUGHOUT / ESU R: 0.726 / ESU R Free: 0.256 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 23.997 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.48→53.81 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|