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- PDB-3scy: Crystal structure of a putative 6-phosphogluconolactonase (BF1038... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3scy | ||||||
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Title | Crystal structure of a putative 6-phosphogluconolactonase (BF1038) from Bacteroides fragilis NCTC 9343 at 1.50 A resolution | ||||||
![]() | Hypothetical bacterial 6-phosphogluconolactonase | ||||||
![]() | HYDROLASE / 7-bladed beta-propeller / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY | ||||||
Function / homology | ![]() Lactonase, 7-bladed beta propeller / Lactonase, 7-bladed beta-propeller / Cytochrome cd1-nitrite reductase-like, haem d1 domain superfamily / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta Similarity search - Domain/homology | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Joint Center for Structural Genomics (JCSG) | ||||||
![]() | ![]() Title: Crystal structure of a Hypothetical bacterial 6-phosphogluconolactonase (BF1038) from Bacteroides fragilis NCTC 9343 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 | ![]() | 158.1 KB | Display | ![]() |
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PDB format | ![]() | 125.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 418.4 KB | Display | ![]() |
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Full document | ![]() | 419.5 KB | Display | |
Data in XML | ![]() | 17.9 KB | Display | |
Data in CIF | ![]() | 27.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-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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Components
#1: Protein | Mass: 39293.371 Da / Num. of mol.: 1 / Fragment: sequence database residues 25-384 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||||
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#2: Chemical | ChemComp-UNL / Num. of mol.: 1 / Source method: obtained synthetically | ||||||
#3: Chemical | #4: Chemical | ChemComp-NA / | #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 | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 36.76 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 30.00% polyethylene glycol 4000, 0.20M magnesium chloride, 0.1M TRIS pH 8.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 22, 2011 / Details: double crystal monochromator | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.5→27.054 Å / Num. obs: 50531 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 21.616 Å2 / Rmerge(I) obs: 0.034 / Net I/σ(I): 17.52 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() 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. MAGNESIUM (MG) AND SODIUM (NA) FROM THE CRYSTALLIZATION AND PURIFICATIONS SOLUTIONS RESPECTIVELY HAVE BEEN MODELED INTO THE STRUCTURE. 4. AN UNNOWN LIGAND (UNL) HAS BEEN MODELED INTO THE PUTATIVE ACTIVE SITE. 5. THE REFINEMENT WAS RESTRAINED AGAINST THE MAD PHASES.
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Displacement parameters | Biso max: 100.58 Å2 / Biso mean: 28.6549 Å2 / Biso min: 13.1 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→27.054 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.54 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -7.6948 Å / Origin y: 29.625 Å / Origin z: 16.3729 Å
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Refinement TLS group | Selection details: chain A |