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Yorodumi- PDB-3c26: Crystal structure of a putative acetyltransferase (NP_394282.1) f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3c26 | ||||||
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Title | Crystal structure of a putative acetyltransferase (NP_394282.1) from Thermoplasma acidophilum at 2.00 A resolution | ||||||
Components | Putative acetyltransferase Ta0821 | ||||||
Keywords | TRANSFERASE / NP_394282.1 / A Putative Acetyltransferase / Acetyltransferase (GNAT) family / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thermoplasma acidophilum DSM 1728 (acidophilic) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of a putative acetyltransferase (NP_394282.1) from Thermoplasma acidophilum at 2.00 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 | 3c26.cif.gz | 66.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3c26.ent.gz | 51.6 KB | Display | PDB format |
PDBx/mmJSON format | 3c26.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3c26_validation.pdf.gz | 448.8 KB | Display | wwPDB validaton report |
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Full document | 3c26_full_validation.pdf.gz | 450.9 KB | Display | |
Data in XML | 3c26_validation.xml.gz | 13.5 KB | Display | |
Data in CIF | 3c26_validation.cif.gz | 19 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c2/3c26 ftp://data.pdbj.org/pub/pdb/validation_reports/c2/3c26 | 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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-Components
#1: Protein | Mass: 30989.602 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermoplasma acidophilum DSM 1728 (acidophilic) Species: Thermoplasma acidophilum / Strain: DSM 1728 / AMRC-C165 / IFO 15155 / JCM 9062 / Gene: NP_394282.1, Ta0821 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q9HJZ0 | ||||||
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#2: Chemical | #3: Chemical | ChemComp-EDO / #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 | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.85 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.8 Details: NANODROP, 0.2M NaNO3, 20.0% PEG 3350, No Buffer pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97895 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 9, 2007 / Details: Flat mirror (vertical focusing) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Single crystal Si(111) bent (horizontal focusing) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97895 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2→29.488 Å / Num. obs: 17927 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 23.54 Å2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 10.53 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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→29.488 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.918 / SU B: 8.552 / SU ML: 0.123 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.195 / ESU R Free: 0.18 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 RECORD CONTAINS RESIDUAL B FACTORS ONLY. 4. THERE IS AN UNKNOWN DENSITY NEAR HIS 140. 5. NO3 AND EDO WERE MODELED BASED ON CRYSTALLIZATION AND CRYOPROTECTION CONDITIONS.
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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: 22.439 Å2
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Refinement step | Cycle: LAST / Resolution: 2→29.488 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 32.647 Å / Origin y: 29.627 Å / Origin z: 17.476 Å
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