[English] 日本語
Yorodumi- PDB-2eit: Crystal analysis of delta1-pyrroline-5-carboxylate dehydrogenase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2eit | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal analysis of delta1-pyrroline-5-carboxylate dehydrogenase from Thermus thermophilus with bound L-alanine and NAD | ||||||
Components | 1-pyrroline-5-carboxylate dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / Enzyme-coenzyme-inhibitor ternary complex / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information L-glutamate gamma-semialdehyde dehydrogenase / oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor / nucleotide binding Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.65 Å | ||||||
Authors | Inagaki, E. / Sakamoto, K. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal structure analysis of delta1-pyrroline-5-carboxylate dehydrogenase in ternary complex with inhibitor and NAD Authors: Inagaki, E. / Ohshima, N. / Sakamoto, K. / Yokoyama, S. / Tahirov, T.H. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2eit.cif.gz | 237.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2eit.ent.gz | 189.3 KB | Display | PDB format |
PDBx/mmJSON format | 2eit.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ei/2eit ftp://data.pdbj.org/pub/pdb/validation_reports/ei/2eit | HTTPS FTP |
---|
-Related structure data
Related structure data | 2eiwC 2ej6C 2ejdC 2ejlC 2j40S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
| ||||||||
Details | The biological assembly would be a dimer in the asymmetric unit. |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 57113.906 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: PET11A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5SI02, EC: 1.5.1.12 |
---|
-Non-polymers , 6 types, 924 molecules
#2: Chemical | ChemComp-ACT / #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-MPD / ( #7: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.22 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.2 Details: 30% MPD, 50MM SODIUM CITRATE/HCL, 5mM NAD+, 50mM L-alanine, 50MM SODIUM Acetate, pH 5.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Jul 8, 2006 / Details: mirrors |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→30 Å / Num. all: 128737 / Num. obs: 128737 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 14.5 Å2 / Rmerge(I) obs: 0.065 / Rsym value: 0.058 / Net I/σ(I): 22.4 |
Reflection shell | Resolution: 1.65→1.69 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 2.5 / Num. unique all: 8480 / Rsym value: 0.189 / % possible all: 98.4 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 2j40 Resolution: 1.65→27.96 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.528 / SU ML: 0.054 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.092 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 mean: 13.978 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→27.96 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.649→1.691 Å / Total num. of bins used: 20
|