+Open data
-Basic information
Entry | Database: PDB / ID: 1ojt | ||||||
---|---|---|---|---|---|---|---|
Title | STRUCTURE OF DIHYDROLIPOAMIDE DEHYDROGENASE | ||||||
Components | SURFACE PROTEIN | ||||||
Keywords | OXIDOREDUCTASE / REDOX-ACTIVE CENTER / GLYCOLYSIS / NAD / FLAVOPROTEIN / FAD / P64K | ||||||
Function / homology | Function and homology information dihydrolipoyl dehydrogenase / dihydrolipoyl dehydrogenase activity / flavin adenine dinucleotide binding Similarity search - Function | ||||||
Biological species | Neisseria meningitidis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT, MIR / Resolution: 2.75 Å | ||||||
Authors | Li De La Sierra, I. / Prange, T. / Pernot, L. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1997 Title: Molecular structure of the lipoamide dehydrogenase domain of a surface antigen from Neisseria meningitidis. Authors: Li de la Sierra, I. / Pernot, L. / Prange, T. / Saludjian, P. / Schiltz, M. / Fourme, R. / Padron, G. #1: Journal: J.Mol.Biol. / Year: 1994 Title: Crystallization and Preliminary X-Ray Investigation of a Recombinant Outer Membrane Protein from Neisseria Meningitidis Authors: Li De La Sierra, I. / Prange, T. / Fourme, R. / Padron, G. / Fuentes, P. / Musacchio, A. / Madrazo, J. #2: Journal: Proteins / Year: 1992 Title: The Refined Crystal Structure of Pseudomonas Putida Lipoamide Dehydrogenase Complexed with Nad+ at 2.45 A Resolution Authors: Mattevi, A. / Obmolova, G. / Sokatch, J.R. / Betzel, C. / Hol, W.G. #3: Journal: J.Mol.Biol. / Year: 1991 Title: Refined Crystal Structure of Lipoamide Dehydrogenase from Azotobacter Vinelandii at 2.2 A Resolution. A Comparison with the Structure of Glutathione Reductase Authors: Mattevi, A. / Schierbeek, A.J. / Hol, W.G. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1ojt.cif.gz | 104.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1ojt.ent.gz | 81.4 KB | Display | PDB format |
PDBx/mmJSON format | 1ojt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ojt_validation.pdf.gz | 469.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1ojt_full_validation.pdf.gz | 516.4 KB | Display | |
Data in XML | 1ojt_validation.xml.gz | 18.4 KB | Display | |
Data in CIF | 1ojt_validation.cif.gz | 26.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oj/1ojt ftp://data.pdbj.org/pub/pdb/validation_reports/oj/1ojt | HTTPS FTP |
-Related structure data
Related structure data | 1lvlS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 50737.961 Da / Num. of mol.: 1 / Fragment: DIHYDROLIPOAMIDE DEHYDROGENASE DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria meningitidis (bacteria) / Gene: M-6 OBTAINED FROM A GENOMIC / Gene (production host): M-6 OBTAINED FROM A GENOMIC / Production host: Escherichia coli (E. coli) / Strain (production host): HB101 / References: UniProt: Q51225 |
---|---|
#2: Chemical | ChemComp-FAD / |
#3: Water | ChemComp-HOH / |
Compound details | THE ORIGINAL RECOMBINANT PROTEIN CONTAINS THE TWO DOMAINS E2 AND E3 OF THE DEHYDROGENASE ...THE ORIGINAL RECOMBINAN |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
---|
-Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 55 % Description: MIR USED 2 DERIVATIVES, ONE MERCURY (TAMM) IN 3 SITES, AND ONE XENON (PRESSURE = 15 BAR) IN 2 SITES. THE TWO MR AND MIR MAPS WERE COMBINED WITH SIGMAA PROGRAM (CCP4) AND SOLVENT ...Description: MIR USED 2 DERIVATIVES, ONE MERCURY (TAMM) IN 3 SITES, AND ONE XENON (PRESSURE = 15 BAR) IN 2 SITES. THE TWO MR AND MIR MAPS WERE COMBINED WITH SIGMAA PROGRAM (CCP4) AND SOLVENT FLATTENED WITH DM (CCP4) AND SOLOMON PROGRAMS. | ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Method: vapor diffusion, hanging drop / pH: 7 Details: BRIGHT YELLOW CRYSTALS WERE GROWN IN 24-WELL LINBRO PLATES USING HANGING DROP DIFFUSION METHOD AT ROOM TEMPERATURE. RESERVOIR: 1 ML CONTAINING 0.1M POTASSIUM PHOSPHATE AND 2M AMMONIUM ...Details: BRIGHT YELLOW CRYSTALS WERE GROWN IN 24-WELL LINBRO PLATES USING HANGING DROP DIFFUSION METHOD AT ROOM TEMPERATURE. RESERVOIR: 1 ML CONTAINING 0.1M POTASSIUM PHOSPHATE AND 2M AMMONIUM SULFATE (PH 7.0). PRISM CRYSTALS TYPICALLY IN TWO WEEKS AT ROOM TEMPERATURE., vapor diffusion - hanging drop THE E3 DOMAIN (117-601) CRYSTALLIZES IN AMMONIUM SULFATE. IT INCLUDES A FAD COFACTOR BUT NOT THE NADH. THE E3 DOMAIN (117-601) CRYSTALLIZES IN AMMONIUM SULFATE. IT INCLUDE A FAD COFACTOR BUT NOT THE NADH. Temp details: room temp | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.2 / Method: vapor diffusion, hanging dropDetails: Li De La Sierra, I., (1994) J.Mol.Biol., 235, 1154. | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 277 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: LURE / Type: LURE / Wavelength: 0.91 |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Details: MULTILAYER MIRROR |
Radiation | Monochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→40 Å / Num. obs: 11724 / % possible obs: 94 % / Observed criterion σ(I): 3 / Redundancy: 7 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 18 |
Reflection shell | Resolution: 2.7→2.9 Å / Redundancy: 4 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 4 / % possible all: 70 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT, MIR Starting model: DLDH OF PSEUDOMONAS PUTIDA, PDB ENTRY 1LVL. Resolution: 2.75→18 Å / Details: X-PLOR ALSO WAS USED. /
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.75→18 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: PROLSQ / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 5 Å / Rfactor all: 0.201 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |