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- PDB-3gya: Crystal structure of putative acetyltransferase (YP_001815201.1) ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3gya | ||||||
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Title | Crystal structure of putative acetyltransferase (YP_001815201.1) from EXIGUOBACTERIUM SP. 255-15 at 1.62 A resolution | ||||||
![]() | GCN5-related N-acetyltransferase | ||||||
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Function / homology | ![]() acyltransferase activity, transferring groups other than amino-acyl groups Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Joint Center for Structural Genomics (JCSG) | ||||||
![]() | ![]() Title: Crystal structure of putative acetyltransferase (YP_001815201.1) from EXIGUOBACTERIUM SP. 255-15 at 1.62 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 48.1 KB | Display | ![]() |
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PDB format | ![]() | 36.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 17201.553 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: Exig_2736, YP_001815201.1 / Plasmid: SpeedET / Production host: ![]() ![]() ![]() | ||||||
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#2: Chemical | ChemComp-COA / ![]() | ||||||
#3: Chemical | ![]() #4: Chemical | ChemComp-EDO / | ![]() #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: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.82 % |
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Crystal grow![]() | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 3.2M ammonium sulfate, 0.1M MES pH 6.0, Additive: 0.001 M acetyl Co-enzyme A, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 21, 2008 / Details: Vertical focusing mirror | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Single crystal Si(311) bent monochromator (horizontal focusing) Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.62→27.896 Å / Num. obs: 20813 / % possible obs: 99 % / Redundancy: 3.9 % / Biso Wilson estimate: 19.242 Å2 / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 12.3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing![]() | Method: ![]() |
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Processing
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Refinement | Method to determine structure![]() ![]() Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 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. TLS GROUPS WERE ASSIGNED WITH THE AID OF THE TLSMD SERVER. 5. ACETYL COENZYME A WAS INCLUDED AS AN ADDITIVE FOR CRYSTALLIZATION. WE SEE NO DENSITY FOR THE ACETYL GROUP AND HAVE MODELED IT IN THE STRUCTURE AS COENZYME A. THE PANTHOTHENATE AND BETA-MERCAPTOETHYLAMINE MOIETIES OF THE CO-A ARE DISORDERED AND A DOMINANT CONFORMATION HAS BEEN MODELED. THE PEPTIDE LINKING THE PANTHOTHENATE AND BETA-MERCAPTOETHYLAMINE IN CONFORMER A HAS BEEN BUILT IN A DIFFERENT ORIENTATION THAN IN THE MODEL FOR THE RELATED PH 9 STRUCTURE. WHILE THIS APPEARS PLAUSIBLE, GIVEN THE AMBIGUITY IN THE DENSITY FOR THIS REGION, NO CONCLUSIONS SHOULD BE DRAWN WITH HIGH CONFIDENCE. 6. THREE SULFATE IONS AND ONE ETHYLENE GLYCOL MOLECULE FROM THE CRYSTALLIZATION AND CRYOPROTECTION CONDITIONS HAVE BEEN MODELED IN 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 max: 82.8 Å2 / Biso mean: 28.794 Å2 / Biso min: 13.19 Å2
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Refinement step | Cycle: LAST / Resolution: 1.62→27.896 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.62→1.662 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 |
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