[English] 日本語
Yorodumi- PDB-2f9f: Crystal Structure of the Putative Mannosyl Transferase (wbaZ-1)fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2f9f | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of the Putative Mannosyl Transferase (wbaZ-1)from Archaeoglobus fulgidus, Northeast Structural Genomics Target GR29A. | ||||||
Components | first mannosyl transferase (wbaZ-1) | ||||||
Keywords | TRANSFERASE / alpha-beta protein / Structural Genomics / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | Glycosyl transferase, family 1 / Glycosyl transferases group 1 / Glycogen Phosphorylase B; / transferase activity / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / : / First mannosyl transferase (WbaZ-1) Function and homology information | ||||||
Biological species | Archaeoglobus fulgidus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å | ||||||
Authors | Zhou, W. / Forouhar, F. / Conover, K. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of the Putative Mannosyl Transferase (wbaZ-1)from Archaeoglobus fulgidus Authors: Zhou, W. / Forouhar, F. / Conover, K. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2f9f.cif.gz | 44.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2f9f.ent.gz | 34.2 KB | Display | PDB format |
PDBx/mmJSON format | 2f9f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f9/2f9f ftp://data.pdbj.org/pub/pdb/validation_reports/f9/2f9f | HTTPS FTP |
---|
-Related structure data
Similar structure data | |
---|---|
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 20679.221 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Strain: DSM 4304 / Gene: wbaZ-1 / Plasmid: JM109 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: GenBank: 11497664, UniProt: O30192*PLUS |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.71 Å3/Da / Density % sol: 28.406 % |
---|---|
Crystal grow | Temperature: 293 K / pH: 4.6 Details: 100 mM sodium acetate, 25% PEG 4k, 200 mM ammonium sulfate, and 5 mM DTT, pH 4.6, Microbatch, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97915 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 16, 2005 / Details: Mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30.3 Å / Num. all: 13624 / Num. obs: 13624 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.6 % / Biso Wilson estimate: 9.8 Å2 / Rmerge(I) obs: 0.118 / Rsym value: 0.094 / Net I/σ(I): 26.86 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 11.8 % / Rmerge(I) obs: 0.432 / Mean I/σ(I) obs: 7.04 / Num. unique all: 1323 / Rsym value: 0.412 / % possible all: 100 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 1.8→30.3 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 326462.04 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber / Details: Xtalview was also used for refinement.
| |||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 45.86 Å2 / ksol: 0.395979 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.4 Å2
| |||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→30.3 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
|