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Yorodumi- PDB-1n2i: Crystal Structure of Pantothenate Synthetase from M. tuberculosis... -
+Open data
-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 | ||||||
Components | pantothenate synthetase | ||||||
Keywords | LIGASE / Structural genomics / Rossmann fold / dimer / intersubunit beta sheet / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC | ||||||
Function / homology | Function and homology information 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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / rigid body refinement into new data / Resolution: 1.7 Å | ||||||
Authors | Wang, S. / Eisenberg, D. / TB Structural Genomics Consortium (TBSGC) | ||||||
Citation | Journal: Protein Sci. / Year: 2003 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1n2i.cif.gz | 127.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1n2i.ent.gz | 99.7 KB | Display | PDB format |
PDBx/mmJSON format | 1n2i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n2/1n2i ftp://data.pdbj.org/pub/pdb/validation_reports/n2/1n2i | HTTPS FTP |
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-Related structure data
Related structure data | 1mopSC 1n2bC 1n2eC 1n2gC 1n2hC 1n2jC 1n2oC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is a dimer |
-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.) Mycobacterium tuberculosis (bacteria) / Gene: panC / Plasmid: pET30a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P0A5R0, UniProt: P9WIL5*PLUS, pantoate-beta-alanine ligase (AMP-forming) |
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-Non-polymers , 5 types, 412 molecules
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: ROTATING ANODE / Type: RIGAKU FR-D / Wavelength: 1.5418 |
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 |
-Processing
Software |
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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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