[English] 日本語
Yorodumi- PDB-6cvu: Crystal structure of Mycobacterium tuberculosis dethiobiotin synt... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6cvu | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Mycobacterium tuberculosis dethiobiotin synthetase in complex with cytidine | ||||||
Components | ATP-dependent dethiobiotin synthetase BioD | ||||||
Keywords | TRANSFERASE / enzyme / synthetase / nucleotide triphosphate binding | ||||||
Function / homology | Function and homology information dethiobiotin synthase / dethiobiotin synthase activity / biotin biosynthetic process / magnesium ion binding / ATP binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.426 Å | ||||||
Authors | Thompson, A.P. / Wegener, K.L. / Bruning, J.B. / Polyak, S.W. | ||||||
Funding support | Australia, 1items
| ||||||
Citation | Journal: Acs Catalysis / Year: 2018 Title: Mycobacterium tuberculosis Dethiobiotin Synthetase Facilitates Nucleoside Triphosphate Promiscuity through Alternate Binding Modes Authors: Thompson, A.P. / Salaemae, W. / Pederick, J.L. / Abell, A.D. / Booker, G.W. / Bruning, J.B. / Polyak, S.W. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6cvu.cif.gz | 179.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6cvu.ent.gz | 140.5 KB | Display | PDB format |
PDBx/mmJSON format | 6cvu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6cvu_validation.pdf.gz | 3.6 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6cvu_full_validation.pdf.gz | 3.6 MB | Display | |
Data in XML | 6cvu_validation.xml.gz | 36.6 KB | Display | |
Data in CIF | 6cvu_validation.cif.gz | 51.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cv/6cvu ftp://data.pdbj.org/pub/pdb/validation_reports/cv/6cvu | HTTPS FTP |
-Related structure data
Related structure data | 6cveC 6cvfC 6cvvC 6czbC 6czcC 6czeC C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 23473.914 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: bioD, Rv1570, MTCY336.33c / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A5U2S7, UniProt: P9WPQ5*PLUS #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-CTN / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 50.95 % |
---|---|
Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 1.0 - 1.5M (NH4)2SO4, 0.1M Tris pH 8, 10 - 25% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å | ||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 4, 2017 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 2.426→46.49 Å / Num. obs: 35265 / % possible obs: 99.8 % / Redundancy: 10.7 % / Biso Wilson estimate: 53.96 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.022 / Rrim(I) all: 0.071 / Net I/σ(I): 18 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Phasing
Phasing | Method: molecular replacement |
---|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.426→38.44 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.14
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 139.37 Å2 / Biso mean: 56.8988 Å2 / Biso min: 27.78 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.426→38.44 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12
|