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- PDB-3l2h: Crystal structure of Putative sugar phosphate isomerase (AFE_0303... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3l2h | ||||||
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Title | Crystal structure of Putative sugar phosphate isomerase (AFE_0303) from Acidithiobacillus ferrooxidans ATCC 23270 at 1.85 A resolution | ||||||
![]() | Putative sugar phosphate isomerase | ||||||
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Function / homology | ![]() ![]() ![]() ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Joint Center for Structural Genomics (JCSG) | ||||||
![]() | ![]() Title: Crystal structure of Putative sugar phosphate isomerase (AFE_0303) from Acidithiobacillus ferrooxidans ATCC 23270 at 1.85 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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PDBx/mmCIF format | ![]() | 161.7 KB | Display | ![]() |
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PDB format | ![]() | 133.6 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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Details | ANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A TETRAMER AS A SIGNIFICANT OLIGOMERIZATION STATE. |
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Components
#1: Protein | Mass: 18515.168 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 23270 / DSM 14882 / NCIB 8455 / Gene: AFE_0303, AFE_2805 / Plasmid: SpeedET / Production host: ![]() ![]() ![]() #2: Chemical | ![]() #3: Chemical | ChemComp-CXS / ![]() #4: Chemical | ChemComp-EDO / ![]() #5: Water | ChemComp-HOH / | ![]() Sequence details | THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATI | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.34 Å3/Da / Density % sol: 63.16 % 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: 10.5 | Details: 0.2000M sodium chloride, 20.0000% polyethylene glycol 8000, 0.1M CAPS pH 10.5, 0.001 M alpha-ketoglutaric acid, 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: Jul 8, 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: 1.85→29.488 Å / Num. obs: 84481 / % possible obs: 96.3 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 24.678 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 10.11 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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.ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY 3.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY 3.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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4.N-CYCLOHEXYL-3-AMINOPROPANESULFONIC ACID (CXS) FROM CRYSTALLIZATION AND ETHYLENE GLYCOL MOLECULES(EDO) FROM CRYOPROTECTANT ARE MODELED IN THE STRUCTURE, RESPECTIVELY.
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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: 75.98 Å2 / Biso mean: 21.563 Å2 / Biso min: 9.39 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→29.488 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 1586 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 1.85→1.898 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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