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Yorodumi- PDB-3bln: Crystal structure of acetyltransferase GNAT family (NP_981174.1) ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3bln | ||||||
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Title | Crystal structure of acetyltransferase GNAT family (NP_981174.1) from Bacillus cereus ATCC 10987 at 1.31 A resolution | ||||||
Components | Acetyltransferase GNAT family | ||||||
Keywords | TRANSFERASE / NP_981174.1 / acetyltransferase GNAT family / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bacillus cereus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.31 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of acetyltransferase GNAT family (NP_981174.1) from Bacillus cereus ATCC 10987 at 1.31 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
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Remark 999 | SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bln.cif.gz | 82.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bln.ent.gz | 65.2 KB | Display | PDB format |
PDBx/mmJSON format | 3bln.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3bln_validation.pdf.gz | 448.8 KB | Display | wwPDB validaton report |
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Full document | 3bln_full_validation.pdf.gz | 450.7 KB | Display | |
Data in XML | 3bln_validation.xml.gz | 10.4 KB | Display | |
Data in CIF | 3bln_validation.cif.gz | 14.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bl/3bln ftp://data.pdbj.org/pub/pdb/validation_reports/bl/3bln | HTTPS FTP |
-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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Details | SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION. |
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 16298.877 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus cereus (bacteria) / Strain: ATCC 10987 / Gene: NP_981174.1, BCE_4881 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q72YY9 |
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-Non-polymers , 5 types, 189 molecules
#2: Chemical | ChemComp-ACT / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-GOL / | #5: Chemical | ChemComp-MPD / ( | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.54 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: NANODROP, 10.0% Glycerol, 35.0% MPD, 0.1M Acetate pH 4.5, 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-D / Wavelength: 0.91840, 0.97953, 0.97939 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 26, 2007 / Details: Adjustable focusing mirrors in K-B geometry | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) Double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.31→28.63 Å / Num. obs: 34064 / % possible obs: 95.4 % / Redundancy: 3.3 % / Biso Wilson estimate: 12.24 Å2 / Rmerge(I) obs: 0.103 / Rsym value: 0.103 / Net I/σ(I): 2.1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.31→28.63 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.482 / SU ML: 0.028 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.052 / ESU R Free: 0.05 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. ACT, GOL AND MPD MODELED BASED ON CRYSTALLIZATION CONDITION. 4. UNEXPLAINED ELECTRON DENSITY NEAR RESIDUE A 40 WAS NOT 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 mean: 11.328 Å2
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Refinement step | Cycle: LAST / Resolution: 1.31→28.63 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.31→1.344 Å / Total num. of bins used: 20
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