[English] 日本語
Yorodumi- PDB-1xxo: X-ray crystal structure of mycobacterium tuberculosis pyridoxine ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1xxo | ||||||
---|---|---|---|---|---|---|---|
Title | X-ray crystal structure of mycobacterium tuberculosis pyridoxine 5'-phosphate oxidase at 1.8 a resolution | ||||||
Components | hypothetical protein Rv1155 | ||||||
Keywords | OXIDOREDUCTASE / PYRIDOXINE 5'-PHOSPHATE / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC | ||||||
Function / homology | Function and homology information vitamin B6 metabolic process / coenzyme F420 binding / oxidoreductase activity, acting on the CH-CH group of donors / Oxidoreductases / pyridoxal phosphate binding / FMN binding / protein homodimerization activity / cytosol Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å | ||||||
Authors | Biswal, B.K. / Cherney, M.M. / Wang, M. / Garen, C. / James, M.N.G. / TB Structural Genomics Consortium (TBSGC) | ||||||
Citation | Journal: To be Published Title: X-ray crystal structure of mycobacterium tuberculosis pyridoxine 5'-phosphate oxidase at 1.8 a resolution Authors: Biswal, B.K. / Cherney, M.M. / Wang, M. / Garen, C. / James, M.N.G. | ||||||
History |
| ||||||
Remark 400 | COMPOUND SUBUNIT A IN ENTRY 1XXO CORRESPOND TO SUBUNIT B IN 1Y30 AND 2AQ6 AND VICE VERSA |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1xxo.cif.gz | 72.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1xxo.ent.gz | 54.9 KB | Display | PDB format |
PDBx/mmJSON format | 1xxo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1xxo_validation.pdf.gz | 436 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1xxo_full_validation.pdf.gz | 440.7 KB | Display | |
Data in XML | 1xxo_validation.xml.gz | 16.3 KB | Display | |
Data in CIF | 1xxo_validation.cif.gz | 23.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xx/1xxo ftp://data.pdbj.org/pub/pdb/validation_reports/xx/1xxo | HTTPS FTP |
-Related structure data
Related structure data | |
---|---|
Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 16321.480 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: RV1155 / Plasmid: PET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O06553 #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.4 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 12% PEG 8000, 8% ethylene glycerol, 25 mM potassium fluoride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.339794, 1.105523, 1.033204 | ||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 19, 2004 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
| ||||||||||||
Reflection | Resolution: 1.8→40 Å / Num. obs: 22952 / % possible obs: 92.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Biso Wilson estimate: 11.4 Å2 / Rsym value: 0.063 / Net I/σ(I): 12.9 | ||||||||||||
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 1.4 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 1699 / Rsym value: 0.271 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MAD / Resolution: 1.8→34.74 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1492756.07 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: INITIALLY THE STRUCTURE WAS SOLVED AT 2.2 A BY MAD METHOD WITH Ir AS THE ANOMALOUS SCATTERER. HIGH RESOLUTION DATA UP TO 1.8 A WAS COLLECTED LATER AND THE FINAL STRUCTURE WAS REFINED UP TO 1. ...Details: INITIALLY THE STRUCTURE WAS SOLVED AT 2.2 A BY MAD METHOD WITH Ir AS THE ANOMALOUS SCATTERER. HIGH RESOLUTION DATA UP TO 1.8 A WAS COLLECTED LATER AND THE FINAL STRUCTURE WAS REFINED UP TO 1.8 A. ELECTRON DENSITY WAS NOT OBSERVED FOR AMINO ACID RESIDUES 1-4 OF BOTH CHAINS.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 59.1442 Å2 / ksol: 0.37374 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.1 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→34.74 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|