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Yorodumi- PDB-3rh7: Crystal structure of a putative oxidoreductase (SMa0793) from Sin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3rh7 | ||||||
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Title | Crystal structure of a putative oxidoreductase (SMa0793) from Sinorhizobium meliloti 1021 at 3.00 A resolution | ||||||
Components | Hypothetical oxidoreductase | ||||||
Keywords | OXIDOREDUCTASE / FMN-binding split barrel / Nudix / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-biology | ||||||
Function / homology | Function and homology information Oxidoreductases; Acting on the CH-NH group of donors; With NAD+ or NADP+ as acceptor / FMN binding / oxidoreductase activity Similarity search - Function | ||||||
Biological species | Sinorhizobium meliloti (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of a Hypothetical oxidoreductase (SMa0793) from SINORHIZOBIUM MELILOTI 1021 at 3.00 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 | 3rh7.cif.gz | 655.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3rh7.ent.gz | 547.5 KB | Display | PDB format |
PDBx/mmJSON format | 3rh7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rh/3rh7 ftp://data.pdbj.org/pub/pdb/validation_reports/rh/3rh7 | 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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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 34263.555 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Strain: 1021 / Gene: RA0429, SMa0793 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q92ZM6 #2: Chemical | ChemComp-FMN / Sequence details | THE CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THE CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL 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: 2.61 Å3/Da / Density % sol: 52.91 % Description: DATA WERE SCALED USING XSCALE WITH FRIEDEL PAIRS KEPT AS SEPARATE WHEN COMPUTING R MERGE, COMPLETENESS AND Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.8 | Details: 0.2M LiAcetate, 20.0% PEG-3350, No Buffer pH 7.8, 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: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9796,0.9611,0.9794 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 5, 2011 Details: Rhodium-coated vertical and horizontal focusing mirrors; liquid-nitrogen cooled double crystal Si(111) monochromator | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 3→29.759 Å / Num. obs: 42960 / % possible obs: 94.3 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 78.394 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 10.57 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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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: 3→29.759 Å / Cor.coef. Fo:Fc: 0.9305 / Cor.coef. Fo:Fc free: 0.9062 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0 Details: 1. 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 ...Details: 1. 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. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. FMN WAS MODELED IN FOUR SUBUNITS BASED ON THE DENSITY AND COMPARISON WITH RELATED STRUCTURES. THERE IS SOME UNMODELLED DENSITY NEAR THE MODELED FMN. FMN MAY BE PARTIALLY PRESENT IN THE OTHER TWO SUBUNITS (B/E), BUT IT WAS NOT MODELED. FMN MODELED COULD REPRESENT (ORDERED) PART OF FAD AS SEEN IN OTHER HOMOLOGS. 4. NCS RESTRAINTS WERE APPLIED USING BUSTERS LSSR RESTRAINT REPRESENTATION (-AUTONCS).
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Displacement parameters | Biso max: 188.26 Å2 / Biso mean: 79.5308 Å2 / Biso min: 25.68 Å2
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Refinement step | Cycle: LAST / Resolution: 3→29.759 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.08 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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