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Yorodumi- PDB-3of4: Crystal structure of a FMN/FAD- and NAD(P)H-dependent nitroreduct... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3of4 | ||||||
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Title | Crystal structure of a FMN/FAD- and NAD(P)H-dependent nitroreductase (nfnB, IL2077) from Idiomarina loihiensis L2TR at 1.90 A resolution | ||||||
Components | Nitroreductase | ||||||
Keywords | OXIDOREDUCTASE / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-BIOLOGY | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Idiomarina loihiensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of a FMN/FAD- and NAD(P)H-dependent nitroreductase (nfnB, IL2077) from Idiomarina loihiensis L2TR at 1.90 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3of4.cif.gz | 274.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3of4.ent.gz | 229.1 KB | Display | PDB format |
PDBx/mmJSON format | 3of4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/of/3of4 ftp://data.pdbj.org/pub/pdb/validation_reports/of/3of4 | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | CRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE. |
-Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 23517.121 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Idiomarina loihiensis (bacteria) / Gene: nfnB, IL2077 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q5R179 |
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-Non-polymers , 7 types, 420 molecules
#2: Chemical | #3: Chemical | Num. of mol.: 2 / Source method: obtained synthetically #4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-GOL / #6: Chemical | ChemComp-ACT / | #7: Chemical | ChemComp-FAD / | #8: Water | ChemComp-HOH / | |
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-Details
Sequence details | THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATI |
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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: 2.42 Å3/Da / Density % sol: 49.21 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 1.60M ammonium sulfate, 20.00% Glycerol, 0.1M sodium acetate pH 4.6, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.97920,0.97889 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 10, 2010 / Details: Flat mirror (vertical focusing) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Single crystal Si(111) bent monochromator (horizontal focusing) Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.9→29.197 Å / Num. obs: 52053 / % possible obs: 91.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 24.96 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 11.76 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: MAD |
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-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.9→29.197 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.951 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 5.576 / SU ML: 0.087 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.143 / ESU R Free: 0.129 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 6. ACETATE ION (ACT), GLYCEROL (GOL), AND SULFATE ION (SO4) ARE MODELED FROM THE CRYSTALLIZATION SOLUTION. 7. LIGAND MOLECULES FLAVIN-ADENINE DINUCLEOTIDE (FAD) AND FLAVIN MONONUCLEOTIDE (FMN) ARE MODELED BASED ON DENSITY. 8. AN UNKNOWN LIGAND (UNL) HAS BEEN MODELED NEAR FMN IN CHAINS A AND B. THE UNL RESEMBLES ADENINE MOIETY OF FAD AND OCCUPIES NCS RELATED EQUIVALENT POSITION OF THE SAME IN CHAIN C.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 91.03 Å2 / Biso mean: 36.2008 Å2 / Biso min: 14.15 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→29.197 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.901→1.95 Å / Total num. of bins used: 20
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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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