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Yorodumi- PDB-3fkj: Crystal structure of a putative phosphosugar isomerase (stm_0572)... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3fkj | ||||||
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Title | Crystal structure of a putative phosphosugar isomerase (stm_0572) from salmonella typhimurium lt2 at 2.12 A resolution | ||||||
Components | Putative phosphosugar isomerases | ||||||
Keywords | ISOMERASE / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 | ||||||
Function / homology | Function and homology information glutamine-fructose-6-phosphate transaminase (isomerizing) activity / UDP-N-acetylglucosamine metabolic process / carbohydrate derivative binding / fructose 6-phosphate metabolic process / protein N-linked glycosylation / isomerase activity / cytosol Similarity search - Function | ||||||
Biological species | Salmonella typhimurium LT2 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.12 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of putative phosphosugar isomerase (NP_459564.1) from SALMONELLA TYPHIMURIUM LT2 at 2.12 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 | 3fkj.cif.gz | 144.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fkj.ent.gz | 116.4 KB | Display | PDB format |
PDBx/mmJSON format | 3fkj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fk/3fkj ftp://data.pdbj.org/pub/pdb/validation_reports/fk/3fkj | 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 39359.305 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium LT2 (bacteria) / Gene: NP_459564.1, STM0572 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q8ZR50 #2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | 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: 2.21 Å3/Da / Density % sol: 44.45 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.9 Details: 0.2000M NaThioCyanate, 20.0000% PEG-3350, No Buffer pH 6.9, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.90496,0.97858,0.97824 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 16, 2008 / 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: 2.12→29.323 Å / Num. obs: 38085 / % possible obs: 91.2 % / Observed criterion σ(I): -3 / Redundancy: 5.62 % / Biso Wilson estimate: 34.434 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 12.91 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 2.12→29.323 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.939 / Occupancy max: 1 / Occupancy min: 0.23 / SU B: 10.376 / SU ML: 0.14 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.223 / ESU R Free: 0.179 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 RESIDUAL B FACTORS ONLY. 4. THIOCYANATE (SCN) MODELED ARE PRESENT IN CRYSTALLIZATION CONDITIONS.
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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: 74.17 Å2 / Biso mean: 36.186 Å2 / Biso min: 15.4 Å2
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Refinement step | Cycle: LAST / Resolution: 2.12→29.323 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.12→2.175 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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