[English] 日本語
Yorodumi- PDB-1q52: Crystal Structure of Mycobacterium tuberculosis MenB, a Key Enzym... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1q52 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of Mycobacterium tuberculosis MenB, a Key Enzyme in Vitamin K2 Biosynthesis | ||||||
Components | menBNaphthoate synthase | ||||||
Keywords | LYASE / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC | ||||||
Function / homology | Function and homology information 1,4-dihydroxy-2-naphthoyl-CoA synthase / 1,4-dihydroxy-2-naphthoyl-CoA synthase activity / menaquinone biosynthetic process / protein hexamerization / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Truglio, J.J. / Theis, K. / Feng, Y. / Gajda, R. / Machutta, C. / Tonge, P.J. / Kisker, C. / TB Structural Genomics Consortium (TBSGC) | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 Title: Crystal structure of Mycobacterium tuberculosis MenB, a key enzyme in vitamin K2 biosynthesis. Authors: Truglio, J.J. / Theis, K. / Feng, Y. / Gajda, R. / Machutta, C. / Tonge, P.J. / Kisker, C. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1q52.cif.gz | 689.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1q52.ent.gz | 569.5 KB | Display | PDB format |
PDBx/mmJSON format | 1q52.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q5/1q52 ftp://data.pdbj.org/pub/pdb/validation_reports/q5/1q52 | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
| ||||||||
Details | The asymmetric unit contains 2 biologically active hexamers |
-Components
#1: Protein | Mass: 34731.938 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS References: UniProt: O06414, UniProt: P9WNP5*PLUS, 1,4-dihydroxy-2-naphthoyl-CoA synthase #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.22 % | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: dioxane, ammonium sulfate, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K | ||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 10, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 312176 |
Reflection | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 50 Å / % possible obs: 97.9 % / Num. measured all: 1210072 / Rmerge(I) obs: 0.073 |
Reflection shell | *PLUS Rmerge(I) obs: 0.506 / Mean I/σ(I) obs: 1.8 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.114 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.129 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.313 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→50 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.803→1.849 Å / Total num. of bins used: 20 /
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 50 Å / Rfactor Rfree: 0.218 / Rfactor Rwork: 0.195 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|