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Yorodumi- PDB-8qpo: E. coli NfsB with the unnatural amino acid p-nitrophenylalanine a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8qpo | ||||||
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Title | E. coli NfsB with the unnatural amino acid p-nitrophenylalanine at position 124. | ||||||
Components | Oxygen-insensitive NAD(P)H nitroreductase | ||||||
Keywords | OXIDOREDUCTASE / Nitroreductase / unnatural aminoacid | ||||||
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 DH5[alpha] (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.74 Å | ||||||
Authors | Day, M.A. / White, S.A. / Hyde, E.I. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: To Be Published Title: E. coli NfsB with unnatural amino acids at position 124. Authors: Day, M.A. / White, S.A. / Searle, P.F. / Hyde, E.I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8qpo.cif.gz | 684 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8qpo.ent.gz | 572.1 KB | Display | PDB format |
PDBx/mmJSON format | 8qpo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8qpo_validation.pdf.gz | 2.8 MB | Display | wwPDB validaton report |
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Full document | 8qpo_full_validation.pdf.gz | 2.8 MB | Display | |
Data in XML | 8qpo_validation.xml.gz | 61.3 KB | Display | |
Data in CIF | 8qpo_validation.cif.gz | 83 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qp/8qpo ftp://data.pdbj.org/pub/pdb/validation_reports/qp/8qpo | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 24453.607 Da / Num. of mol.: 8 / Mutation: F124(PPN), 5 aa tag Source method: isolated from a genetically manipulated source Details: Unnatural aminoacid p-nitrophenylalanine at position 124 Source: (gene. exp.) Escherichia coli DH5[alpha] (bacteria) / Strain: DH5a / Gene: nfsB, dprA, nfnB, nfsI, ntr, b0578, JW0567 / Plasmid: pBAD-NTR-124TAG, pDule-PPN Details (production host): pBAD-NTR-124TAG expresses NfsB with an amber codon at position 124, pDule-PPN contains a uppressor tRNA/aminoacyl-tRNA synthetase pair incorporating PPN at the stop codon Production host: Escherichia coli (strain K12 / DH10B) (bacteria) Strain (production host): DH10B References: UniProt: P38489, Oxidoreductases, 6,7-dihydropteridine reductase #2: Chemical | ChemComp-FMN / #3: Chemical | ChemComp-ACT / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 50.95 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 100 mM sodium acetate, pH 4.6, 15% ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1 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: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.74→29.71 Å / Num. obs: 47766 / % possible obs: 98.21 % / Redundancy: 3.72 % / Rsym value: 0.146 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 2.741→2.812 Å / Redundancy: 3.68 % / Num. unique obs: 3160 / Rsym value: 0.562 / % possible all: 88.8 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.74→29.71 Å / SU B: 22.544 / SU ML: 0.227 / Cross valid method: THROUGHOUT / ESU R Free: 0.305 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Displacement parameters | Biso mean: 10.69 Å2
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Refinement step | Cycle: LAST / Resolution: 2.74→29.71 Å
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LS refinement shell | Resolution: 2.741→2.812 Å
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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