[English] 日本語
Yorodumi- PDB-2gan: Crystal Structure of a Putative Acetyltransferase from Pyrococcus... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2gan | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of a Putative Acetyltransferase from Pyrococcus horikoshii, Northeast Structural Genomics Target JR32. | ||||||
Components | 182aa long hypothetical protein | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / alpha-beta protein. / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pyrococcus horikoshii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å | ||||||
Authors | Forouhar, F. / Abashidze, M. / Jayaraman, S. / Janjua, H. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of a Putative Acetyltransferase from Pyrococcus horikoshii, Northeast Structural Genomics Target JR32. Authors: Forouhar, F. / Abashidze, M. / Jayaraman, S. / Janjua, H. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2gan.cif.gz | 89.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2gan.ent.gz | 73.4 KB | Display | PDB format |
PDBx/mmJSON format | 2gan.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ga/2gan ftp://data.pdbj.org/pub/pdb/validation_reports/ga/2gan | HTTPS FTP |
---|
-Related structure data
Similar structure data | |
---|---|
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 23226.180 Da / Num. of mol.: 2 / Fragment: PH0736 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Gene: PH0736' / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: GenBank: 3257144, UniProt: O58467*PLUS #2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.66 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 10 mM Tris (pH 7.5), 16% PEG3350, 350 mM ammonium sulfate, and 5 mM DTT., VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97904 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 22, 2006 / Details: mirrors. |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97904 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→24.41 Å / Num. all: 49176 / Num. obs: 49028 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 8.7 Å2 / Rmerge(I) obs: 0.09 / Rsym value: 0.072 / Net I/σ(I): 14.72 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 3.85 / Num. unique all: 4895 / Rsym value: 0.275 / % possible all: 99.6 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 2.1→24.41 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 428249.76 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 44.5307 Å2 / ksol: 0.340141 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.4 Å2
| |||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→24.41 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
|