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Yorodumi- PDB-3ec9: CRYSTAL STRUCTURE OF A NTF2-like protein (BTH_I0051) FROM BURKHOL... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ec9 | ||||||
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Title | CRYSTAL STRUCTURE OF A NTF2-like protein (BTH_I0051) FROM BURKHOLDERIA THAILANDENSIS E264 AT 1.60 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 | 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 / ACETATE ION / SnoaL-like domain-containing protein Function and homology information | ||||||
Biological species | Burkholderia thailandensis E264 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of NTF2-like protein of unknown function (YP_440611.1) from Burkholderia thailandensis E264 at 1.60 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 | 3ec9.cif.gz | 74.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ec9.ent.gz | 59 KB | Display | PDB format |
PDBx/mmJSON format | 3ec9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ec9_validation.pdf.gz | 443.9 KB | Display | wwPDB validaton report |
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Full document | 3ec9_full_validation.pdf.gz | 443.9 KB | Display | |
Data in XML | 3ec9_validation.xml.gz | 16.1 KB | Display | |
Data in CIF | 3ec9_validation.cif.gz | 24.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ec/3ec9 ftp://data.pdbj.org/pub/pdb/validation_reports/ec/3ec9 | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 16149.042 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia thailandensis E264 (bacteria) Gene: YP_440611.1, BTH_I0051 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q2T2I4 #2: Chemical | ChemComp-ACT / #3: Chemical | ChemComp-GOL / | #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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.16 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 0.2000M Ca(OAc)2, 20.0000% PEG-8000, 0.1M MES pH 6.0, 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: BL9-2 / Wavelength: 0.91162,0.97932,0.97920 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Aug 3, 2008 / Details: Flat collimating mirror, toroid focusing mirror | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.6→27.875 Å / Num. obs: 40560 / % possible obs: 99.9 % / Redundancy: 3.6 % / Biso Wilson estimate: 14.705 Å2 / Rmerge(I) obs: 0.092 / Rsym value: 0.092 / Net I/σ(I): 5.825 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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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: 1.6→27.875 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.943 / Occupancy max: 1 / Occupancy min: 0.37 / SU B: 2.874 / SU ML: 0.052 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.083 / ESU R Free: 0.084 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 ...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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. (3). ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. (4). ACETATE (ACT) IONS FROM THE CRYSTALLIZATION SOLUTION AND A GLYCEROL (GOL) MOLECULE FROM CRYO SOLUTION WERE MODELED.
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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: 62.81 Å2 / Biso mean: 16.976 Å2 / Biso min: 5.99 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→27.875 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.642 Å / Total num. of bins used: 20
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Refinement TLS params. | S12: -0.0093 Å ° / Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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