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- PDB-3h4o: Crystal structure of a nitroreductase family protein (cd3355) fro... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3h4o | ||||||
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Title | Crystal structure of a nitroreductase family protein (cd3355) from clostridium difficile 630 at 1.50 A resolution | ||||||
![]() | NITROREDUCTASE FAMILY PROTEIN | ||||||
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Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Joint Center for Structural Genomics (JCSG) | ||||||
![]() | ![]() Title: Crystal structure of NITROREDUCTASE FAMILY PROTEIN (YP_001089872.1) from CLOSTRIDIUM DIFFICILE 630 at 1.50 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 57.9 KB | Display | ![]() |
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PDB format | ![]() | 43.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Details | SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION. |
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Components
#1: Protein | Mass: 22310.746 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-FMN / ![]() |
#3: Chemical | ChemComp-MPD / (![]() |
#4: Chemical | ChemComp-MRD / (![]() |
#5: Water | ChemComp-HOH / ![]() |
Sequence details | THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATI |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 46.89 % Description: DATA WERE SCALED USING XSCALE WITH FRIEDEL PAIRS KEPT AS SEPARATE WHEN COMPUTING R-SYM, COMPLETENESS AND . Crystal grow | ![]() Temperature: 277 K / Method: vapor diffusion, sitting drop | Details: 35.0000% Dioxane, 0.001 M flavin mononucleotide (FMN), NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
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-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 22, 2009 / 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: 1.5→29.348 Å / Num. obs: 32401 / % possible obs: 96.6 % / Observed criterion σ(I): -3 / Redundancy: 3 % / Biso Wilson estimate: 12.217 Å2 Rfree details: DATA WERE SCALED USING XSCALE WITH FRIEDEL PAIRS KEPT AS SEPARATE WHEN COMPUTING R-SYM, COMPLETENESS AND . Rmerge(I) obs: 0.052 / Net I/σ(I): 9.97 Reflection shell |
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-Phasing
Phasing![]() | Method: ![]() |
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Processing
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Refinement | Method to determine structure![]() ![]() 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. A FLAVIN MONONUCLEOTIDE (FMN) MOLECULE IS MODELED INTO THE PUTATIVE ACTIVE SITE ON EACH SUBUNIT. THE FMN RESTRAINTS WERE CHANGED TO ALLOW BENDING OF THE ISOALLOXAZINE RING ALONG THE N5-N10 VIRTUAL AXIS RESULTING IN AN IMPROVED FIT BETWEEN THE FMN COORDINATES AND ELECTRON DENSITY. 4. (4S)- and (4R)-2-METHYL-2,4-PENTANEDIOL (MPD / MRD) MOLECULES WERE MODELED BASED ON THE CRYOPROTECTION CONDITION.
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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 max: 57.68 Å2 / Biso mean: 15.258 Å2 / Biso min: 3.62 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→29.348 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.501→1.539 Å / Total num. of bins used: 20
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