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- PDB-1mop: Crystal Structure of a Pantothenate Synthetase from M. tuberculosis -
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Open data
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Basic information
Entry | Database: PDB / ID: 1mop | ||||||
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Title | Crystal Structure of a Pantothenate Synthetase from M. tuberculosis | ||||||
![]() | 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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Remark 999 | SEQUENCE Residue 2 is an alanine in the sequence. Mutation of this residue was necessary to ...SEQUENCE Residue 2 is an alanine in the sequence. Mutation of this residue was necessary to generate an NcoI restriction site for cloning into the expression vector pET30a. The last 9 residues after Arg300 were cleaved off by enterokinase digestion (unintentionally), which was carried out to cleave the N-terminal tag from the recombinant protein. |
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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 | ![]() | 100.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 468.3 KB | Display | ![]() |
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Full document | ![]() | 472.3 KB | Display | |
Data in XML | ![]() | 26.6 KB | Display | |
Data in CIF | ![]() | 39.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1n2bC ![]() 1n2eC ![]() 1n2gC ![]() 1n2hC ![]() 1n2iC ![]() 1n2jC ![]() 1n2oC ![]() 1ihoS 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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1 |
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2 | ![]()
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Unit cell |
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Details | The biological assembly is a dimer. |
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Components
#1: Protein | Mass: 31500.100 Da / Num. of mol.: 2 / Mutation: A2T,E77G Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P0A5R0, UniProt: P9WIL5*PLUS, pantoate-beta-alanine ligase (AMP-forming) #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-EOH / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG3000, lithium sulfate, magnesium sulfate, imidazole, ethanol, glycerol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 4, 2002 / Details: mirrors |
Radiation | Monochromator: Ni Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→80 Å / Num. all: 64100 / Num. obs: 64100 / % possible obs: 89.1 % / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Biso Wilson estimate: 25.5 Å2 / Rmerge(I) obs: 0.049 / Rsym value: 0.049 / Net I/σ(I): 36.4 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.312 / Mean I/σ(I) obs: 4.4 / Num. unique all: 3664 / Rsym value: 0.312 / % possible all: 51.1 |
Reflection | *PLUS Lowest resolution: 80 Å |
Reflection shell | *PLUS % possible obs: 51.1 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1IHO Resolution: 1.6→19.81 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 51.6452 Å2 / ksol: 0.37523 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→19.81 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.7 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 1.6 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.211 / Rfactor Rwork: 0.192 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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