[English] 日本語
Yorodumi- PDB-1n2e: Crystal Structure of a Pantothenate Synthetase from M. tuberculos... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1n2e | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of a Pantothenate Synthetase from M. tuberculosis in complex with AMPCPP and pantoate | ||||||
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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / rigid body refinement into new data / Resolution: 1.6 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 |
| ||||||
Remark 600 | HETEROGEN Entry 1N2B and this entry (1N2E) are two different experiments that together indicate ...HETEROGEN Entry 1N2B and this entry (1N2E) are two different experiments that together indicate that AMPCPP and pantoate cannot occupy the same active site simultaneously. The crystal for entry 1N2E was soaked in pantoate and AMPCPP overnight, and partial occupancy of AMPCPP and pantoate in subunit A was observed. The crystal for entry 1N2B was soaked in twice concentration of pantoate and same concentration of AMPCPP for over 24 hours, and this gave higher occupancy of pantoate, but lower occupancy of AMPCPP in subunit A. Both entries have full occupancy of AMPCPP in subunit B with a glycerol at the pantoate binding site. The structural difference between the two entries is higher occupancy of pantoate and lower occupancy of AMPCPP in subunit A of 1N2B relative to that of 1N2E. | ||||||
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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1n2e.cif.gz | 130.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1n2e.ent.gz | 100.6 KB | Display | PDB format |
PDBx/mmJSON format | 1n2e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1n2e_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1n2e_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 1n2e_validation.xml.gz | 26.8 KB | Display | |
Data in CIF | 1n2e_validation.cif.gz | 39.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n2/1n2e ftp://data.pdbj.org/pub/pdb/validation_reports/n2/1n2e | HTTPS FTP |
-Related structure data
Related structure data | 1mopSC 1n2bC 1n2gC 1n2hC 1n2iC 1n2jC 1n2oC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
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) |
---|
-Non-polymers , 7 types, 420 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-PAF / | #5: Chemical | #6: Chemical | ChemComp-EOH / #7: Chemical | ChemComp-MG / | #8: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.81 % |
---|---|
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 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-D / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 6, 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: 1.6→50 Å / Num. all: 67182 / Num. obs: 67182 / % possible obs: 93.7 % / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Biso Wilson estimate: 27.8 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 25.2 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.463 / Mean I/σ(I) obs: 2.6 / Num. unique all: 4197 / Rsym value: 0.463 / % possible all: 58.8 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: rigid body refinement into new data Starting model: PDB entry 1MOP Resolution: 1.6→19.82 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: full occupancy of AMPCPP in subunit B, partial occupancy of AMPCPP and pantoate in subunit A, at 1.6 A resolution.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 50.7372 Å2 / ksol: 0.377103 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.5 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→19.82 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.6→1.7 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|