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Yorodumi- PDB-3bem: Crystal structure of putative nitroreductase ydfN (2632848) from ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3bem | ||||||
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Title | Crystal structure of putative nitroreductase ydfN (2632848) from Bacillus subtilis at 1.65 A resolution | ||||||
Components | Putative NAD(P)H nitroreductase ydfN | ||||||
Keywords | OXIDOREDUCTASE / 2632848 / putative nitroreductase ydfN / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / Flavoprotein / FMN / NAD / NADP | ||||||
Function / homology | Function and homology information Oxidoreductases / : / response to toxic substance / oxidoreductase activity / cytoplasm Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.65 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of putative nitroreductase ydfN (2632848) from Bacillus subtilis at 1.65 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
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Remark 999 | SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHH. THE CONSTRUCT WAS ... SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHH. THE CONSTRUCT WAS ENGINEERED WITH THE FOLLOWING MUTATIONS: RESIDUES LYS 147, GLU 148, AND LYS 149 WERE MUTATED TO ALA. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bem.cif.gz | 108.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bem.ent.gz | 86.2 KB | Display | PDB format |
PDBx/mmJSON format | 3bem.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3bem_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 3bem_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 3bem_validation.xml.gz | 21.6 KB | Display | |
Data in CIF | 3bem_validation.cif.gz | 31.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/be/3bem ftp://data.pdbj.org/pub/pdb/validation_reports/be/3bem | HTTPS FTP |
-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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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 25392.166 Da / Num. of mol.: 2 / Mutation: K147A, E148A, K149A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: 2632848, ydfN, BSU05480 / Plasmid: MH4a / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: P96692, Oxidoreductases |
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-Non-polymers , 5 types, 341 molecules
#2: Chemical | ChemComp-NI / | ||||
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#3: Chemical | ChemComp-ACT / | ||||
#4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
-Details
Sequence details | REMARK 999 SEQUENCE: THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION REMARK 999 TAG MGSDKIHHHHHH. ...REMARK 999 SEQUENCE: THE 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: 2.14 Å3/Da / Density % sol: 42.48 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: NANODROP, 40.0% 1,2-propanediol, 0.1M Acetate pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.91840, 0.97939, 0.97953 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 26, 2007 / Details: Adjustable focusing mirrors in K-B geometry | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) Double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.65→28.583 Å / Num. obs: 51334 / % possible obs: 97 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 27.797 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 8.98 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.65→28.583 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.963 / SU B: 2.982 / SU ML: 0.052 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.086 / ESU R Free: 0.083 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. 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. 3. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 4. ACETATE AND 1,2-PROPANEDIOL WERE MODELED BASED ON CRYSTALLIZATION CONDITIONS. 5. NI MODELED BASED ON GEOMETRY AND COORDINATION ENVIRONMENT. 6. FMN MODELED BASED ON DENSITY AND PROPOSED FUNCTION.
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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: 17.273 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→28.583 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.69 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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