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Open data
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Basic information
Entry | Database: PDB / ID: 2hlh | ||||||
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Title | Crystal structure of fucosyltransferase NodZ from Bradyrhizobium | ||||||
![]() | Nodulation fucosyltransferase | ||||||
![]() | TRANSFERASE / glycosyltransferase / fucosyltransferase / NodZ / nodulation | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Brzezinski, K. / Stepkowski, T. / Panjikar, S. / Bujacz, G. / Jaskolski, M. | ||||||
![]() | ![]() 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. #1: ![]() Title: Cloning, purification, crystallization and preliminary crystallographic studies of Bradyrhizobium fucosyltransferase NodZ Authors: Brzezinski, K. / Rogozinski, B. / Stepkowski, T. / Bujacz, G. / Jaskolski, M. #2: ![]() 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. #3: ![]() 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. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 81.8 KB | Display | ![]() |
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PDB format | ![]() | 59.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 413.7 KB | Display | ![]() |
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Full document | ![]() | 414 KB | Display | |
Data in XML | ![]() | 8 KB | Display | |
Data in CIF | ![]() | 13 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2hhcSC ![]() 2ocxC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components on special symmetry positions |
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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 | ||
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#2: Chemical | ChemComp-PO4 / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.25 % |
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Crystal grow | Temperature: 277 K / pH: 7.5 Details: 0.25M potassium dihydrogen phosphate, 0.1M Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K, pH 7.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Nov 20, 2004 |
Radiation | Monochromator: SI DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.02 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→15 Å / Num. obs: 30716 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 11.7 % / Biso Wilson estimate: 24.2 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 58.2 |
Reflection shell | Resolution: 1.95→2.01 Å / Redundancy: 11.7 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 11.9 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2HHC Resolution: 1.95→15 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.933 / SU B: 4.447 / SU ML: 0.07 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.116 / ESU R Free: 0.12 / Stereochemistry target values: ENGH & HUBER Details: THE REFINEMENT INCLUDED TLS PARAMETERS. RESIDUES 179-192, 245-256, 305-308 AND 318-330 WERE NOT MODELED DUE TO LACK OF ELECTRON DENSITY. THERE WAS NO OBSERVED ELECTRON DENSITY FOR SIDE CHAIN ...Details: THE REFINEMENT INCLUDED TLS PARAMETERS. RESIDUES 179-192, 245-256, 305-308 AND 318-330 WERE NOT MODELED DUE TO LACK OF ELECTRON DENSITY. THERE WAS NO OBSERVED ELECTRON DENSITY FOR SIDE CHAIN ATOMS OF RESIDUES 3, 47, 48, 118, 119, 122, 153, 178, 193, 196, 218, 227, 244, 258, 259, 262, 283, 303, 304, 310. THOSE ATOMS WERE MODELED WITH ZERO OCCUPANCY AND B-FACTOR OF 70 A2.
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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 mean: 27.03 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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