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- PDB-1n2i: Crystal Structure of Pantothenate Synthetase from M. tuberculosis... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1n2i | ||||||
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Title | Crystal Structure of Pantothenate Synthetase from M. tuberculosis in complex with a reaction intermediate, pantoyl adenylate, different occupancies of pantoyl adenylate | ||||||
![]() | pantothenate synthetase | ||||||
![]() | LIGASE / Structural genomics / Rossmann fold / dimer / intersubunit beta sheet / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC | ||||||
Function / homology | ![]() beta-alanine metabolic process / pantoate-beta-alanine ligase (AMP-forming) / pantoate-beta-alanine ligase activity / pantothenate biosynthetic process / manganese ion binding / magnesium ion binding / ATP binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Wang, S. / Eisenberg, D. / TB Structural Genomics Consortium (TBSGC) | ||||||
![]() | ![]() Title: Crystal structures of a pantothenate synthetase from M. tuberculosis and its complexes with substrates and a reaction intermediate Authors: Wang, S. / Eisenberg, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 127.9 KB | Display | ![]() |
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PDB format | ![]() | 99.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 986.1 KB | Display | ![]() |
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Full document | ![]() | 990.4 KB | Display | |
Data in XML | ![]() | 26.4 KB | Display | |
Data in CIF | ![]() | 38.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1mopSC ![]() 1n2bC ![]() 1n2eC ![]() 1n2gC ![]() 1n2hC ![]() 1n2jC ![]() 1n2oC S: Starting model for refinement C: citing same article ( |
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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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Unit cell |
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Details | The biological assembly is a dimer |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 31500.100 Da / Num. of mol.: 2 / Mutation: T2A, E77G Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P0A5R0, UniProt: P9WIL5*PLUS, pantoate-beta-alanine ligase (AMP-forming) |
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-Non-polymers , 5 types, 412 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/PAJ.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/EOH.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PAJ.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/EOH.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-GOL / | #5: Chemical | ChemComp-EOH / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.62 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG3000, lithium sulfate, magnesium chloride, imidazol, ethanol, glycerol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 3, 2002 / Details: mirrors |
Radiation | Monochromator: Ni Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. all: 58966 / Num. obs: 58966 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 7.5 % / Biso Wilson estimate: 25.4 Å2 / Rmerge(I) obs: 0.077 / Rsym value: 0.077 / Net I/σ(I): 23.7 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.489 / Mean I/σ(I) obs: 2.9 / Num. unique all: 5586 / Rsym value: 0.489 / % possible all: 94.1 |
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Processing
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Refinement | Method to determine structure: rigid body refinement into new data Starting model: PDB entry 1MOP Resolution: 1.7→19.8 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: The occupancies for the ligands were not refined. They are inferred from the temperature factors of the ligand atoms, which were refined with an occupancy of 1.00 for all atoms. The pantoyl ...Details: The occupancies for the ligands were not refined. They are inferred from the temperature factors of the ligand atoms, which were refined with an occupancy of 1.00 for all atoms. The pantoyl adenylate molecule in subunit B has an average temperature factor similar to that of the nearby protein atoms in the active site. However, that in subunit A has a much higher average temperature factor.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 48.7665 Å2 / ksol: 0.373287 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→19.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.81 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file |
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