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Yorodumi- PDB-1idt: STRUCTURAL STUDIES ON A PRODRUG-ACTIVATING SYSTEM-CB1954 AND FMN-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1idt | ||||||
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Title | STRUCTURAL STUDIES ON A PRODRUG-ACTIVATING SYSTEM-CB1954 AND FMN-DEPENDENT NITROREDUCTASE | ||||||
Components | MINOR FMN-DEPENDENT NITROREDUCTASE | ||||||
Keywords | OXIDOREDUCTASE / FMN / bioreductive activation / prodrug | ||||||
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 Å | ||||||
Authors | Johansson, E. / Parkinson, G.N. / Denny, W.A. / Neidle, S. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2003 Title: Studies on the Nitroreductase Prodrug-Activating System. Crystal Structures of Complexes with the Inhibitor Dicoumarol and Dinitrobenzamide Prodrugs and of the Enzyme Active Form. Authors: Johansson, E. / Parkinson, G.N. / Denny, W.A. / Neidle, S. | ||||||
History |
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Remark 600 | HETEROGEN FMN 1218 AND CB1 1219 ARE ASSOCIATED WITH CHAIN A. FMN 2218 AND CB1 2219 ARE ASSOCIATED ...HETEROGEN FMN 1218 AND CB1 1219 ARE ASSOCIATED WITH CHAIN A. FMN 2218 AND CB1 2219 ARE ASSOCIATED WITH CHAIN B. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1idt.cif.gz | 102.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1idt.ent.gz | 78.4 KB | Display | PDB format |
PDBx/mmJSON format | 1idt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1idt_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 1idt_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 1idt_validation.xml.gz | 20.8 KB | Display | |
Data in CIF | 1idt_validation.cif.gz | 28.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/id/1idt ftp://data.pdbj.org/pub/pdb/validation_reports/id/1idt | HTTPS FTP |
-Related structure data
Related structure data | 1oo5C 1oo6C 1oonC 1ooqC 1ds7S S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 23937.182 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: NFNB OR NFSI OR NFSB OR NTR OR DPRA OR B0578 / Species (production host): Escherichia coli / Production host: Escherichia coli B (bacteria) / Strain (production host): B / References: UniProt: P38489, 1.6.99.7 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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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: 2.3 Å3/Da / Density % sol: 46.55 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 4.6 Details: PEG 4000, sodium acetate , pH 4.6, VAPOR DIFFUSION, temperature 277K |
-Data collection
Diffraction | Mean temperature: 97 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.976262 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 3, 2000 |
Radiation | Monochromator: germanium 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976262 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. all: 31534 / Num. obs: 28476 / % possible obs: 90.34 % / Observed criterion σ(F): 0 / Redundancy: 13.14 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 29.76 |
Reflection shell | Resolution: 2→2.07 Å / Rmerge(I) obs: 0.201 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1DS7 Resolution: 2→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 29.2792 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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LS refinement shell |
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