+Open data
-Basic information
Entry | Database: PDB / ID: 2z0z | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of putative acetyltransferase | ||||||
Components | Putative uncharacterized protein TTHA1799 | ||||||
Keywords | TRANSFERASE / alpha/beta protein / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information acyltransferase activity, transferring groups other than amino-acyl groups / identical protein binding Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Murayama, K. / Kato-Murayama, M. / Terada, T. / Kuramitsu, S. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: Structure / Year: 2009 Title: Genetic Encoding of 3-Iodo-l-Tyrosine in Escherichia coli for Single-Wavelength Anomalous Dispersion Phasing in Protein Crystallography Authors: Sakamoto, K. / Murayama, K. / Oki, K. / Iraha, F. / Kato-Murayama, M. / Takahashi, M. / Ohtake, K. / Kobayashi, T. / Kuramitsu, S. / Shirouzu, M. / Yokoyama, S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2z0z.cif.gz | 60.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2z0z.ent.gz | 42.9 KB | Display | PDB format |
PDBx/mmJSON format | 2z0z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z0/2z0z ftp://data.pdbj.org/pub/pdb/validation_reports/z0/2z0z | HTTPS FTP |
---|
-Related structure data
Related structure data | 2z10C 2zxvC 2z11S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 22162.570 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) References: UniProt: Q5SHD1, ribosomal-protein-alanine N-acetyltransferase | ||
---|---|---|---|
#2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.3 Å3/Da / Density % sol: 62.71 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 1M ammonium sulphate, 15% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 18, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 19707 / % possible obs: 96.8 % / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Biso Wilson estimate: 11.7 Å2 / Rsym value: 0.038 / Net I/σ(I): 39.1 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 8.1 / Num. unique all: 1470 / Rsym value: 0.216 / % possible all: 73.6 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2Z11 Resolution: 2→30.95 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1505725.43 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 56.3419 Å2 / ksol: 0.366532 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.1 Å2
| ||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→30.95 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||
Xplor file |
|