[English] 日本語
Yorodumi- PDB-2z1y: Crystal structure of LysN, alpha-aminoadipate aminotransferase (c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2z1y | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of LysN, alpha-aminoadipate aminotransferase (complexed with N-(5'-phosphopyridoxyl)-L-leucine), from Thermus thermophilus HB27 | ||||||
Components | Alpha-aminodipate aminotransferase | ||||||
Keywords | TRANSFERASE / alpha-aminoadipate aminotransferase / thermus thermophilus / substrate specifity | ||||||
Function / homology | Function and homology information 2-aminoadipate transaminase / 2-aminoadipate transaminase activity / lysine biosynthetic process via aminoadipic acid / pyridoxal phosphate binding Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Tomita, T. / Miyazaki, T. / Miyagawa, T. / Fushinobu, S. / Kuzuyama, T. / Nishiyama, M. | ||||||
Citation | Journal: To be Published Title: Mechanism of broad substrate specificity of alpha-aminoadipate aminotransferase from Thermus thermophilus Authors: Tomita, T. / Miyazaki, T. / Miyagawa, T. / Fushinobu, S. / Kuzuyama, T. / Nishiyama, M. #1: Journal: Microbiology / Year: 2004 Title: alpha-Aminoadipate aminotransferase from an extremely thermophilic bacterium, Thermus thermophilus Authors: Miyazaki, T. / Miyazaki, J. / Yamane, H. / Nishiyama, M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2z1y.cif.gz | 157.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2z1y.ent.gz | 125.1 KB | Display | PDB format |
PDBx/mmJSON format | 2z1y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z1/2z1y ftp://data.pdbj.org/pub/pdb/validation_reports/z1/2z1y | HTTPS FTP |
---|
-Related structure data
Related structure data | 2dtv S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 43899.738 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB27 / Gene: lysN / Plasmid: pET-LysN7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Codon-plus(DE3) / References: UniProt: Q72LL6, 2-aminoadipate transaminase #2: Chemical | #3: Chemical | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.38 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 18% PEG 4000, 0.1M Tris-HCl (pH 7.0), 0.2M lithium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.978 Å |
Detector | Type: ADSC QUAMTUM 4r / Detector: CCD / Date: Apr 22, 2007 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→50 Å / Num. all: 81957 / Num. obs: 81957 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 15.6 Å2 / Rmerge(I) obs: 0.109 / Rsym value: 0.109 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 1.75→1.81 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.323 / Mean I/σ(I) obs: 2.8 / Num. unique all: 8113 / Rsym value: 0.323 / % possible all: 100 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2DTV 2dtv Resolution: 1.75→36.83 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 3739265.57 / 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: 45.7883 Å2 / ksol: 0.336658 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.5 Å2
| |||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→36.83 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 1.75→1.86 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
| |||||||||||||||||||||||||
Xplor file |
|