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Yorodumi- PDB-2r1i: Crystal structure of putative acetyltransferase (YP_831484.1) fro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2r1i | ||||||
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Title | Crystal structure of putative acetyltransferase (YP_831484.1) from Arthrobacter sp. FB24 at 1.65 A resolution | ||||||
Components | GCN5-related N-acetyltransferase | ||||||
Keywords | TRANSFERASE / YP_831484.1 / Putative acetyltransferase / Arthrobacter sp. FB24 / Acetyltransferase (GNAT) family / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Arthrobacter sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.65 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of putative acetyltransferase (YP_831484.1) from Arthrobacter sp. FB24 at 1.65 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
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Remark 300 | BIOMOLECULE: 1 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION ... BIOMOLECULE: 1 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON BURIED SURFACE AREA. CRYSTAL STRUCTURE PACKING SUGGESTS THAT THE BIOLOGICALLY RELEVANT FORM IS A DIMER. SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE. | ||||||
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 FOLLOWED BY THE TARGET SEQUENCE. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2r1i.cif.gz | 82.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2r1i.ent.gz | 63.7 KB | Display | PDB format |
PDBx/mmJSON format | 2r1i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2r1i_validation.pdf.gz | 461.6 KB | Display | wwPDB validaton report |
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Full document | 2r1i_full_validation.pdf.gz | 465.8 KB | Display | |
Data in XML | 2r1i_validation.xml.gz | 18.1 KB | Display | |
Data in CIF | 2r1i_validation.cif.gz | 26.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r1/2r1i ftp://data.pdbj.org/pub/pdb/validation_reports/r1/2r1i | 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: ARG / End label comp-ID: LEU / Refine code: 6 / Auth seq-ID: 25 - 171 / Label seq-ID: 26 - 172
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Details | SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE. |
-Components
#1: Protein | Mass: 18600.143 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arthrobacter sp. (bacteria) / Strain: FB24 / Gene: YP_831484.1, Arth_2003 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: A0JWG4 #2: Chemical | ChemComp-CL / | #3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | |
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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: 2.65 Å3/Da / Density % sol: 53.51 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: NANODROP, 15.0% Glycerol, 8.5% Isopropanol, 17.0% PEG 4000, 0.1M HEPES pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837, 0.97929, 0.97905 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 1, 2007 / Details: Flat mirror (vertical focusing) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Single crystal Si(111) bent (horizontal focusing) Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.65→27.746 Å / Num. obs: 46392 / % possible obs: 89.7 % / Biso Wilson estimate: 31.781 Å2 / Rmerge(I) obs: 0.027 / Net I/σ(I): 13.07 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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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: 1.65→27.746 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.956 / SU B: 3.519 / SU ML: 0.061 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.086 / ESU R Free: 0.088 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS 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 RECORD CONTAINS 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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. ETHYLENE GLYCOL USED AS A CRYOPROTECTANT, CHLORIDE ANION AND GLYCEROL MOLECULES FROM THE CRYSTALLIZATION BUFFER WERE MODELED INTO THE STRUCTURE.
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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: 24.404 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→27.746 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1849 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 1.65→1.692 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 | Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth seq-ID: 16 - 171 / Label seq-ID: 17 - 172
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