[English] 日本語
![](img/lk-miru.gif)
- PDB-3siw: Crystal structure of NodZ alpha-1,6-fucosyltransferase co-crystal... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3siw | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of NodZ alpha-1,6-fucosyltransferase co-crystallized with GDP | ||||||
![]() | Nodulation fucosyltransferase NodZ | ||||||
![]() | TRANSFERASE / family GT23 glycosyltransferase / GT-B fold / alfa1 / 6-fucosyltransferase / nodulation protein / chitooligosaccharide fucosylation / Nod Factor biosynthesis / nitrogen fixation / legume-rhizobium symbiosis | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Brzezinski, K. / Dauter, Z. / Jaskolski, M. | ||||||
![]() | ![]() Title: Structures of NodZ alpha-1,6-fucosyltransferase in complex with GDP and GDP-fucose Authors: Brzezinski, K. / Dauter, Z. / Jaskolski, M. #1: ![]() Title: High-resolution structure of NodZ fucosyltransferase involved in the biosynthesis of the nodulation factor Authors: Brzezinski, K. / Stepkowski, T. / Panjikar, S. / Bujacz, G. / Jaskolski, M. #2: ![]() Title: Structure and Mechanism of Helicobacter pylori Fucosyltransferase: A basis for lipopolysaccharide variation and inhibitor design Authors: Sun, H.Y. / Lin, S.W. / Ko, T.P. / Liu, C.L. / Wang, H.J. / Lin, C.H. #3: ![]() Title: Crystal structure of human alpha 1,6-fucosyltransferase, FUT8 Authors: Ihara, H. / Ikeda, Y. / Toma, S. / Wang, X. / Suzuki, T. / Gu, J. / Miyoshi, E. / Tsukihara, T. / Honke, K. / Matsumoto, A. / Nakagawa, A. / Taniguchi, N. #4: ![]() Title: Cloning, purification, crystallization and preliminary crystallographic studies of bradyrhizobium fucosyltransferase NodZ Authors: Brzezinski, K. / Rogozinski, B. / Stepkowski, T. / Bujacz, G. / Jaskolski, M. #5: ![]() Title: Bacterial nodulation protein NodZ is a chitin oligosaccharide fucosyltransferase which can also recognize related substrates of animal origin Authors: Quinto, C. / Wijfjes, A.H. / Bloemberg, G.V. / Blok-Tip, L. / Lopez-Lara, I.M. / Lugtenberg, B.J. / Thomas-Oates, J.E. / Spaink, H.P. #6: ![]() Title: Rhizobium sp. strain NGR234 NodZ protein is a fucosyltransferase Authors: Quesada-Vincens, D. / Fellay, R. / Nasim, T. / Viprey, V. / Burger, U. / Prome, J.C. / Broughton, W.J. / Jabbouri, S. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 143 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 111.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 784.2 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 787.1 KB | Display | |
Data in XML | ![]() | 15.6 KB | Display | |
Data in CIF | ![]() | 22.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3sixC ![]() 2hhcS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | Mass: 37828.988 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9AQ17, Transferases; Glycosyltransferases; Hexosyltransferases | ||
---|---|---|---|
#2: Chemical | ChemComp-GDP / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.88 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 400 mM KH2PO4 100 mM MES pH 6.5 5 mM MgCl2 2 mM GDP 1 mM Chitopentaose, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 1, 2010 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Rosenbaum-Rock double-crystal Si(220) monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.98→50 Å / Num. all: 30810 / Num. obs: 30783 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 9.8 % / Biso Wilson estimate: 24.6 Å2 / Rmerge(I) obs: 0.119 / Χ2: 1.121 / Net I/σ(I): 16.6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
|
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2HHC Resolution: 1.98→46.73 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.934 / WRfactor Rfree: 0.2293 / WRfactor Rwork: 0.1805 / Occupancy max: 1 / Occupancy min: 0.1 / FOM work R set: 0.8736 / SU B: 5.68 / SU ML: 0.085 / SU R Cruickshank DPI: 0.1309 / SU Rfree: 0.1317 / Cross valid method: R-FREE / σ(F): 0 / ESU R Free: 0.132 / Stereochemistry target values: Engh & Huber Details: HYDROGEN ATOMS WERE ADDED AT RIDING POSITIONS, U VALUES: WITH TLS ADDED
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 89.07 Å2 / Biso mean: 32.892 Å2 / Biso min: 11.49 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.98→46.73 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.98→2.031 Å / Total num. of bins used: 20
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|