[English] 日本語
Yorodumi- PDB-1l7e: Crystal Structure of R. rubrum Transhydrogenase Domain I with Bou... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1l7e | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of R. rubrum Transhydrogenase Domain I with Bound NADH | ||||||
Components | nicotinamide nucleotide Transhydrogenase, subunit alpha 1 | ||||||
Keywords | OXIDOREDUCTASE / Transhydrogenase domain I with NADH bound | ||||||
Function / homology | Function and homology information NAD(P)+ transhydrogenase (Si-specific) activity / proton-translocating NAD(P)+ transhydrogenase activity / proton-translocating NAD(P)+ transhydrogenase / NADPH regeneration / NADH binding / NAD+ binding / NAD binding / NADP binding / protein dimerization activity / plasma membrane Similarity search - Function | ||||||
Biological species | Rhodospirillum rubrum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Prasad, G.S. / Wahlberg, M. / Sridhar, V. / Yamaguchi, M. / Hatefi, Y. / Stout, C.D. | ||||||
Citation | Journal: Biochemistry / Year: 2002 Title: Crystal Structures of Transhydrogenase Domain I with and without Bound NADH Authors: Prasad, G.S. / Wahlberg, M. / Sridhar, V. / Yamaguchi, M. / Hatefi, Y. / Stout, C.D. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1l7e.cif.gz | 289.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1l7e.ent.gz | 228.5 KB | Display | PDB format |
PDBx/mmJSON format | 1l7e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1l7e_validation.pdf.gz | 556.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1l7e_full_validation.pdf.gz | 603.6 KB | Display | |
Data in XML | 1l7e_validation.xml.gz | 34.9 KB | Display | |
Data in CIF | 1l7e_validation.cif.gz | 54.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l7/1l7e ftp://data.pdbj.org/pub/pdb/validation_reports/l7/1l7e | HTTPS FTP |
-Related structure data
Related structure data | 1l7dSC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 40324.785 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodospirillum rubrum (bacteria) / Production host: Escherichia coli (E. coli) References: UniProt: Q60164, UniProt: Q2RSB2*PLUS, EC: 1.6.1.1 #2: Chemical | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.32 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 7.5 Details: mPEG 2K, Tris-HCl, Magnesium acetate, NADH, pH 7.5, VAPOR DIFFUSION, temperature 277.0K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.965 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 21, 2001 |
Radiation | Monochromator: Curved crystal (silicon 111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.965 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. all: 326796 / Num. obs: 102189 / % possible obs: 99.4 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 30.9 Å2 / Rsym value: 0.119 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 1.9→1.95 Å / Redundancy: 3 % / Mean I/σ(I) obs: 1.5 / Rsym value: 0.375 / % possible all: 99.4 |
Reflection | *PLUS Num. measured all: 326796 / Rmerge(I) obs: 0.119 |
Reflection shell | *PLUS Rmerge(I) obs: 0.375 |
-Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1L7D Resolution: 1.9→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→50 Å
| ||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |