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- PDB-3c3e: Crystal structure of 2-phospho-(S)-lactate transferase from Metha... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3c3e | ||||||
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Title | Crystal structure of 2-phospho-(S)-lactate transferase from Methanosarcina mazei in complex with Fo and GDP. Northeast Structural Genomics Consortium target MaR46 | ||||||
![]() | 2-phospho-L-lactate transferase | ||||||
![]() | TRANSFERASE / alpha-beta protein / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / Magnesium | ||||||
Function / homology | ![]() 2-phospho-L-lactate transferase / LPPG:FO 2-phospho-L-lactate transferase activity / F420-0 metabolic process / magnesium ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Forouhar, F. / Abashidze, M. / Xu, H. / Grochowski, L.L. / Seetharaman, J. / Hussain, M. / Kuzin, A.P. / Chen, Y. / Zhou, W. / Xiao, R. ...Forouhar, F. / Abashidze, M. / Xu, H. / Grochowski, L.L. / Seetharaman, J. / Hussain, M. / Kuzin, A.P. / Chen, Y. / Zhou, W. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Galinier, A. / White, R.H. / Tong, L. / Northeast Structural Genomics Consortium (NESG) | ||||||
![]() | ![]() Title: Molecular insights into the biosynthesis of the f420 coenzyme. Authors: Forouhar, F. / Abashidze, M. / Xu, H. / Grochowski, L.L. / Seetharaman, J. / Hussain, M. / Kuzin, A. / Chen, Y. / Zhou, W. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Galinier, A. / White, R.H. / 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 | ![]() | 246.9 KB | Display | ![]() |
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PDB format | ![]() | 201 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 2.5 MB | Display | ![]() |
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Full document | ![]() | 2.5 MB | Display | |
Data in XML | ![]() | 51.3 KB | Display | |
Data in CIF | ![]() | 66.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3c3dSC ![]() 3cgwC C: citing same article ( S: Starting model for refinement |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 34838.324 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q8PVT6, Transferases; Transferring phosphorus-containing groups; Transferases for other substituted phosphate groups #2: Chemical | ChemComp-FO1 / #3: Chemical | ChemComp-GDP / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.89 Å3/Da / Density % sol: 74.83 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: Protein solution: 10 mM Tris-HCl pH 7.5, 100 mM NaCl, 5 mM Fo, 5 mM GDP, 5 mM MgCl2, 5 mM DTT. Reservoir solution: 100 mM HEPES pH 6.8, 0.5% PEG 8000, 1.35 M Ammonium sulfate, VAPOR ...Details: Protein solution: 10 mM Tris-HCl pH 7.5, 100 mM NaCl, 5 mM Fo, 5 mM GDP, 5 mM MgCl2, 5 mM DTT. Reservoir solution: 100 mM HEPES pH 6.8, 0.5% PEG 8000, 1.35 M Ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 11, 2005 / Details: Mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97926 Å / Relative weight: 1 |
Reflection | Resolution: 3→28.69 Å / Num. all: 49264 / Num. obs: 49264 / % possible obs: 92.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 84.9 Å2 / Rmerge(I) obs: 0.093 / Rsym value: 0.073 / Net I/σ(I): 12.13 |
Reflection shell | Resolution: 3→3.11 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.368 / Mean I/σ(I) obs: 1.5 / Rsym value: 0.345 / % possible all: 90.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 3C3D Resolution: 3→28.69 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 294429.51 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 49.2239 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 84.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3→28.69 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.11 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 10
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