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- PDB-3fgy: CRYSTAL STRUCTURE OF A NTF2-LIKE PROTEIN (BXE_B1094) FROM BURKHOL... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3fgy | ||||||
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Title | CRYSTAL STRUCTURE OF A NTF2-LIKE PROTEIN (BXE_B1094) FROM BURKHOLDERIA XENOVORANS LB400 AT 1.59 A RESOLUTION | ||||||
![]() | uncharacterized NTF2-like protein | ||||||
![]() | UNKNOWN FUNCTION / NTF2-LIKE PROTEIN / ![]() ![]() | ||||||
Function / homology | ![]() SnoaL-like domain / SnoaL-like domain / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Joint Center for Structural Genomics (JCSG) | ||||||
![]() | ![]() Title: Crystal structure of NTF2-like protein of unknown function. (YP_554211.1) from BURKHOLDERIA XENOVORANS LB400 at 1.59 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 | ![]() | 72.8 KB | Display | ![]() |
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PDB format | ![]() | 57.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-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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Details | AUTHORS STATE THAT CRYSTAL PACKING ANALYSIS AND STATIC LIGHT SCATTERING SUGGEST THAT THIS IS THE STABLE OLIGOMERIC FORM IN SOLUTION. |
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Components
#1: Protein | Mass: 14983.539 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: Bxeno_B1893, Bxe_B1094, YP_554211.1 / Plasmid: SpeedET / Production host: ![]() ![]() ![]() #2: Chemical | Num. of mol.: 2 / Source method: obtained synthetically #3: Chemical | ![]() #4: 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: 2.31 Å3/Da / Density % sol: 46.64 % |
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Crystal grow![]() | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 10.5 Details: 30.0000% PEG-400, 0.1M CAPS pH 10.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 11, 2008 / Details: Adjustable focusing mirrors in K-B geometry | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) Double Crystal Monochrometer / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.59→29.037 Å / Num. obs: 37939 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Biso Wilson estimate: 20.169 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 14.92 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4.PEG MOLECULES (PEG) FROM THE CRYSTALLIZATION CONDITION HAVE BEEN MODELED IN THE SOLVENT STRUCTURE. 5.AN UNIDENITIFIED LIGAND (UNL) HAS BEEN MODELED IN CHAIN B AT WHAT COULD BE THE PUTATIVE ACTIVE SITE BASED ON COMPARISON WITH A LIGAND BOUND IN THE LIMONENE-1,2-EPOXIDE HYDROLASE WITH PDB ACCESSION CODE 1NU3.
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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: 59.11 Å2 / Biso mean: 23.121 Å2 / Biso min: 6.3 Å2
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Refinement step | Cycle: LAST / Resolution: 1.59→29.037 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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