[English] 日本語
Yorodumi- PDB-5lh9: Amine transaminase crystal structure from an uncultivated Pseudom... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5lh9 | ||||||
---|---|---|---|---|---|---|---|
Title | Amine transaminase crystal structure from an uncultivated Pseudomonas species in the PLP-bound (internal aldimine) form | ||||||
Components | OMEGA TRANSAMINASE | ||||||
Keywords | TRANSFERASE / TRANSAMINASE / AMINOTRANSFERASE / PYRIDOXAL PHOSPHATE / PLP-DEPENDENT ENZYME FOLD TYPE 1 | ||||||
Function / homology | Function and homology information beta-alanine-pyruvate transaminase / beta-alanine-pyruvate transaminase activity / : / pyridoxal phosphate binding Similarity search - Function | ||||||
Biological species | Pseudomonas sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Reddem, E. / Thunnissen, A.M.W.H. | ||||||
Citation | Journal: Acs Catalysis / Year: 2017 Title: Explaining Operational Instability of Amine Transaminases: Substrate-Induced Inactivation Mechanism and Influence of Quaternary Structure on Enzyme-Cofactor Intermediate Stability. Authors: Borner, T. / Ramisch, S. / Reddem, E. / Bartsch, S. / Vogel, A. / Thunnissen, A.M.W.H. / Adlercreutz, P. / Grey, C. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5lh9.cif.gz | 961.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5lh9.ent.gz | 816.5 KB | Display | PDB format |
PDBx/mmJSON format | 5lh9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5lh9_validation.pdf.gz | 473.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5lh9_full_validation.pdf.gz | 480.4 KB | Display | |
Data in XML | 5lh9_validation.xml.gz | 65.1 KB | Display | |
Data in CIF | 5lh9_validation.cif.gz | 91.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lh/5lh9 ftp://data.pdbj.org/pub/pdb/validation_reports/lh/5lh9 | HTTPS FTP |
-Related structure data
Related structure data | 5lhaC 3fcrS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||||||||||||||
Unit cell |
| ||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
|
-Components
#1: Protein | Mass: 49570.469 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: Gene obtained by metagenomic library screening / Source: (gene. exp.) Pseudomonas sp. (bacteria) / Production host: Escherichia coli (E. coli) References: UniProt: A0A1W2VMW5*PLUS, beta-alanine-pyruvate transaminase #2: Chemical | ChemComp-PLP / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 Details: Reservoir contained 100 mM sodium malonate, pH 5.0, 12% (w/v) PEG 3350, 4% (v/v) formamide. Protein solution contained 15 mg/ml protein in 50 mM Tris-HCl, pH 8.0, 0.3 M NaCl, 0.5 mM PLP |
---|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.976 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 17, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection twin | Operator: k,h,-l / Fraction: 0.15 |
Reflection | Resolution: 1.95→47.4 Å / Num. obs: 98173 / % possible obs: 98.6 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.108 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 1.95→1.99 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.819 / % possible all: 79.5 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3FCR Resolution: 1.95→47.4 Å / Cross valid method: FREE R-VALUE / σ(F): 0.02 / Phase error: 22.31
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.13 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→47.4 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|