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- PDB-3mgj: Crystal structure of the Saccharop_dh_N domain of MJ1480 protein ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3mgj | ||||||
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Title | Crystal structure of the Saccharop_dh_N domain of MJ1480 protein from Methanococcus jannaschii. Northeast Structural Genomics Consortium Target MjR83a. | ||||||
![]() | Uncharacterized protein MJ1480 | ||||||
![]() | structural genomics / unknown function / Saccharop_dh_N domain / NESG / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium | ||||||
Function / homology | LOR/SDH bifunctional enzyme, conserved domain / Conserved hypothetical protein CHP00300 / LOR/SDH bifunctional enzyme, conserved domain / LOR/SDH bifunctional enzyme conserved region / DHS-like NAD/FAD-binding domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta / Uncharacterized protein MJ1480![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Vorobiev, S. / Neely, H. / Seetharaman, J. / Lee, D. / Patel, D. / Ciccosanti, C. / Xiao, R. / Acton, T.B. / Everett, J.K. / Montelione, G.T. ...Vorobiev, S. / Neely, H. / Seetharaman, J. / Lee, D. / Patel, D. / Ciccosanti, C. / Xiao, R. / Acton, T.B. / Everett, J.K. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG) | ||||||
![]() | ![]() Title: Crystal structure of the Saccharop_dh_N domain of MJ1480 protein from Methanococcus jannaschii. Authors: Vorobiev, S. / Neely, H. / Seetharaman, J. / Lee, D. / Patel, D. / Xiao, R. / Ciccosanti, C. / Acton, T.B. / Everett, J.K. / Montelione, G.T. / Hunt, J.F. / Tong, L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 82.2 KB | Display | ![]() |
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PDB format | ![]() | 67.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 440.9 KB | Display | ![]() |
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Full document | ![]() | 447 KB | Display | |
Data in XML | ![]() | 9.8 KB | Display | |
Data in CIF | ![]() | 12.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Details | Dimer according to aggregation screening |
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Components
#1: Protein | Mass: 14069.513 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: MJ1480 / Plasmid: pET 21-23C / Production host: ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal grow | Temperature: 291 K / Method: microbatch under paraffin oil / pH: 4.2 Details: 2.21M lithium chloride, 0.1M sodium citrate, pH 4.2 , microbatch under paraffin oil, temperature 291K |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 3, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. all: 10525 / Num. obs: 10472 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Rmerge(I) obs: 0.114 / Net I/σ(I): 23.5 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.605 / Mean I/σ(I) obs: 3.8 / Num. unique all: 1053 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.433 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.703→33.155 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Selection details: chain B |