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Yorodumi- PDB-3nre: Crystal structure of a Putative aldose 1-epimerase (b2544) from E... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3nre | ||||||
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Title | Crystal structure of a Putative aldose 1-epimerase (b2544) from ESCHERICHIA COLI K12 at 1.59 A resolution | ||||||
Components | Aldose 1-epimerase | ||||||
Keywords | ISOMERASE / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 | ||||||
Function / homology | Function and homology information aldose 1-epimerase activity / galactose catabolic process via UDP-galactose / glucose metabolic process / carbohydrate binding / DNA damage response / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.59 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of a Putative aldose 1-epimerase (b2544) from ESCHERICHIA COLI K12 at 1.59 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 | 3nre.cif.gz | 509.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3nre.ent.gz | 425.2 KB | Display | PDB format |
PDBx/mmJSON format | 3nre.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3nre_validation.pdf.gz | 464.5 KB | Display | wwPDB validaton report |
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Full document | 3nre_full_validation.pdf.gz | 478.4 KB | Display | |
Data in XML | 3nre_validation.xml.gz | 57 KB | Display | |
Data in CIF | 3nre_validation.cif.gz | 84.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nr/3nre ftp://data.pdbj.org/pub/pdb/validation_reports/nr/3nre | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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4 |
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Unit cell |
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Details | CRYSTAL PACKING ANALYSIS AND ANALYTICAL SIZE-EXCLUSION CHROMATOGRAPHY SUGGEST THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION. |
-Components
#1: Protein | Mass: 32988.941 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: EcDH1_1124 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: C9QPM9, UniProt: P76584*PLUS #2: Chemical | ChemComp-PEG / #3: Chemical | ChemComp-MG / | #4: Water | ChemComp-HOH / | 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: 2.74 Å3/Da / Density % sol: 55.17 % 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 / pH: 8.5 | Details: 0.2000M magnesium chloride, 20.0000% polyethylene glycol 8000, 0.1M TRIS pH 8.5, Additive 0.005M D-GLUCOSE, 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: BL9-2 / Wavelength: 0.95369,0.97936,0.97920 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 10, 2010 / Details: Flat collimating mirror, toroid focusing mirror | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.59→28.544 Å / Num. obs: 189340 / % possible obs: 93.5 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 19.942 Å2 / Rmerge(I) obs: 0.035 / Net I/σ(I): 10.54 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.59→28.544 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.962 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 3.42 / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.076 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 RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4.SOLVENT MOLECULES WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5.PEG-200 AND PEG-8000 FRAGMENTS (PEG) AND MAGNESIUM (MG) FROM THE CRYSTALLIZATION AND CRYOPROTECTANT SOLUTIONS HAVE BEEN MODELED.
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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: 93.78 Å2 / Biso mean: 27.796 Å2 / Biso min: 11.32 Å2
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Refinement step | Cycle: LAST / Resolution: 1.59→28.544 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.59→1.631 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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