[English] 日本語
Yorodumi- PDB-3nwg: The crystal structure of a microcomparments protein from Desulfit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3nwg | ||||||
---|---|---|---|---|---|---|---|
Title | The crystal structure of a microcomparments protein from Desulfitobacterium hafniense DCB | ||||||
Components | Microcompartments proteinBacterial microcompartment | ||||||
Keywords | STRUCTURAL PROTEIN / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / BMC domain | ||||||
Function / homology | Function and homology information Bacterial microcompartment shell protein PduT / BMC (bacterial microcompartment) domain / BMC domain / Bacterial microcompartment domain / CcmK-like superfamily / BMC / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Desulfitobacterium hafniense (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å | ||||||
Authors | Fan, Y. / Volkart, L. / Gu, M. / Axen, S. / Greenleaf, W.B. / Kerfeld, C. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: Structure of a PduT homolog from a novel bacterial microcompartment Authors: Greenleaf, W.B. / Fan, Y. / Axen, S. / Volkart, L. / Gu, M. / Joachimiak, A. / Kerfeld, C. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3nwg.cif.gz | 70.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3nwg.ent.gz | 57.2 KB | Display | PDB format |
PDBx/mmJSON format | 3nwg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nw/3nwg ftp://data.pdbj.org/pub/pdb/validation_reports/nw/3nwg | HTTPS FTP |
---|
-Related structure data
Similar structure data | |
---|---|
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| x 6||||||||
2 |
| ||||||||
Unit cell |
| ||||||||
Details | Size exclusion chromatography confirms the presence of trimers. Two copies of trimer can potentially stack together and form a hexamer, as found in crystal lattice. |
-Components
#1: Protein | Mass: 18957.252 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Desulfitobacterium hafniense (bacteria) Strain: DCB / Gene: Dhaf_0360 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): pPK1037 / References: UniProt: B8G1Q4 | ||
---|---|---|---|
#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.4 Å3/Da / Density % sol: 63.86 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 30% (w/v) PEG400, 0.2M magnesium chloride, 0.1M HEPES at pH7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97937 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 5, 2009 / Details: mirror |
Radiation | Monochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97937 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. all: 7665 / Num. obs: 7665 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 20.4 % / Biso Wilson estimate: 54.77 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 53.1 |
Reflection shell | Resolution: 2.7→2.72 Å / Redundancy: 19.4 % / Rmerge(I) obs: 0.713 / Mean I/σ(I) obs: 4.63 / Num. unique all: 193 / % possible all: 100 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 2.7→50 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.899 / SU B: 25.201 / SU ML: 0.259 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.518 / ESU R Free: 0.335 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 61.863 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→50 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.702→2.772 Å / Total num. of bins used: 20
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 0.6729 Å / Origin y: 40.8598 Å / Origin z: 37.235 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|