+Open data
-Basic information
Entry | Database: PDB / ID: 3bii | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of Activated MPT Synthase | ||||||
Components |
| ||||||
Keywords | TRANSFERASE / MPT synthase / Moco biosynthesis / MoaE / MoaD / ubiquitin-like / beta-hammerhead fold / Molybdenum cofactor biosynthesis | ||||||
Function / homology | Function and homology information molybdopterin adenylyltransferase complex / molybdopterin synthase complex / molybdopterin synthase / molybdopterin synthase activity / Mo-molybdopterin cofactor biosynthetic process / nucleotide binding / protein homodimerization activity / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å | ||||||
Authors | Daniels, J.N. / Schindelin, H. | ||||||
Citation | Journal: Biochemistry / Year: 2008 Title: Crystal structure of a molybdopterin synthase-precursor Z complex: insight into its sulfur transfer mechanism and its role in molybdenum cofactor deficiency. Authors: Daniels, J.N. / Wuebbens, M.M. / Rajagopalan, K.V. / Schindelin, H. #1: Journal: J.Biol.Chem. / Year: 2003 Title: Structural studies of molybdopterin synthase provide insights into its catalytic mechanism Authors: Rudolph, M.J. / Wuebbens, M.M. / Turque, O. / Rajagopalan, K.V. / Schindelin, H. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3bii.cif.gz | 56.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3bii.ent.gz | 44.2 KB | Display | PDB format |
PDBx/mmJSON format | 3bii.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3bii_validation.pdf.gz | 436 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3bii_full_validation.pdf.gz | 437.8 KB | Display | |
Data in XML | 3bii_validation.xml.gz | 11.7 KB | Display | |
Data in CIF | 3bii_validation.cif.gz | 15.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bi/3bii ftp://data.pdbj.org/pub/pdb/validation_reports/bi/3bii | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 8780.944 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: moaD, chlA4, chlM / Plasmid: pET-15b / Cell line (production host): BL21 DE3 / Production host: Escherichia coli (E. coli) / References: UniProt: P30748 | ||
---|---|---|---|
#2: Protein | Mass: 16871.826 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: moaE, chlA5 / Plasmid: pET-15b / Cell line (production host): BL21 DE3 / Production host: Escherichia coli (E. coli) / References: UniProt: P30749 | ||
#3: Chemical | ChemComp-CL / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 43.98 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1.1 Ammonium sulfate and .1M HEPES pH=7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Date: Jan 1, 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: 2.5→50 Å / Num. obs: 9359 / % possible obs: 87.6 % / Rmerge(I) obs: 0.096 / Χ2: 1.505 / Net I/σ(I): 13 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2.5→40 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.891 / SU B: 20.561 / SU ML: 0.243 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.339 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.916 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→40 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.5→2.565 Å / Total num. of bins used: 20
|