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Yorodumi- PDB-3f7s: CRYSTAL STRUCTURE OF A NTF2-LIKE PROTEIN OF UNKNOWN FUNCTION (PP_... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3f7s | ||||||
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Title | CRYSTAL STRUCTURE OF A NTF2-LIKE PROTEIN OF UNKNOWN FUNCTION (PP_4556) FROM PSEUDOMONAS PUTIDA KT2440 AT 2.11 A RESOLUTION | ||||||
Components | uncharacterized NTF2-like protein | ||||||
Keywords | UNKNOWN FUNCTION / NTF2-LIKE PROTEIN / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2 | ||||||
Function / homology | Function and homology information SnoaL-like domain / 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 | Pseudomonas putida KT2440 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.11 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of NTF2-like protein of unknown function (NP_746665.1) from PSEUDOMONAS PUTIDA KT2440 at 2.11 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 | 3f7s.cif.gz | 40.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3f7s.ent.gz | 30.8 KB | Display | PDB format |
PDBx/mmJSON format | 3f7s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f7/3f7s ftp://data.pdbj.org/pub/pdb/validation_reports/f7/3f7s | 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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-Components
#1: Protein | Mass: 16310.308 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida KT2440 (bacteria) / Gene: NP_746665.1, PP4556, PP_4556 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q88EB0 |
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#2: Chemical | ChemComp-UNL / Num. of mol.: 1 / Source method: obtained synthetically |
#3: Chemical | ChemComp-SO4 / |
#4: Chemical | ChemComp-GOL / |
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.98 Å3/Da / Density % sol: 58.68 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 10.5 Details: 0.8000M K2HPO4, 0.2000M Li2SO4, 1.2000M NaH2PO4, 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: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97948 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 13, 2008 / Details: Adjustable focusing mirrors in K-B geometry | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) Double Crystal Monochrometer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97948 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.11→29.476 Å / Num. obs: 11917 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 31.836 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 9.68 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: SAD |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.11→29.476 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.938 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 8.412 / SU ML: 0.099 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.161 / ESU R Free: 0.15 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. GLYCEROL (PRESENT IN THE CRYOPROTECTION CONDITIONS) AND SULFATE (PRESENT IN THE CRYSTALLIZATION SOLUTION) ARE MODELED. THE ASSIGNMENT OF SULFATE IS TENTATIVE AS PHOSPHATE IS ALSO PRESENT IN THE CRYSTALLIZATION SOLUTION. 5. AN UNKNOWN LIGAND (UNL) WAS MODELED INTO THE PUTATVE ACTIVE SITE.
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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: 96.63 Å2 / Biso mean: 33.633 Å2 / Biso min: 13.02 Å2
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Refinement step | Cycle: LAST / Resolution: 2.11→29.476 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.11→2.165 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 11.5692 Å / Origin y: 25.3864 Å / Origin z: 45.0636 Å
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