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- PDB-3six: Crystal structure of NodZ alpha-1,6-fucosyltransferase soaked wit... -

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Basic information

Entry
Database: PDB / ID: 3six
TitleCrystal structure of NodZ alpha-1,6-fucosyltransferase soaked with GDP-fucose
ComponentsNodulation fucosyltransferase NodZ
KeywordsTRANSFERASE / family GT23 glycosyltransferase / GT-B fold / alfa1 / 6-fucosyltransferase / nodulation protein / chitooligosaccharide fucosylation / Nod Factor biosynthesis / nitrogen fixation / legume-rhizobium symbiosis
Function / homology
Function and homology information


oligosaccharide biosynthetic process / hexosyltransferase activity
Similarity search - Function
Nodulation protein Z / Nodulation protein Z (NodZ) / Glycosyltransferase family 23 (GT23) domain / Glycosyltransferase family 23 (GT23) domain profile. / Rossmann fold - #11340 / Rossmann fold - #11350 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / Nodulation fucosyltransferase NodZ
Similarity search - Component
Biological speciesBradyrhizobium sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsBrzezinski, K. / Dauter, Z. / Jaskolski, M.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Structures of NodZ alpha-1,6-fucosyltransferase in complex with GDP and GDP-fucose
Authors: Brzezinski, K. / Dauter, Z. / Jaskolski, M.
#1: Journal: Acta Biochim.Pol. / Year: 2007
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: Journal: J.Biol.Chem. / Year: 2007
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: Journal: Glycobiology / Year: 2007
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: Journal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Cloning, purification, crystallization and preliminary crystallographic studies of bradyrhizobium fucosyltransferase NodZ
Authors: Brzezinski, K. / Rogozinski, B. / Stepkowski, T. / Bujacz, G. / Jaskolski, M.
#5: Journal: Proc.Natl.Acad.Sci.USA / Year: 1997
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: Journal: J. Bacteriol. / Year: 1997
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
DepositionJun 20, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2012Group: Database references
Revision 1.2Nov 8, 2017Group: Database references / Refinement description / Category: citation_author / software / Item: _citation_author.name
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nodulation fucosyltransferase NodZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4034
Polymers37,8291
Non-polymers5743
Water1,47782
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Nodulation fucosyltransferase NodZ
hetero molecules

A: Nodulation fucosyltransferase NodZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,8058
Polymers75,6582
Non-polymers1,1476
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area3570 Å2
ΔGint-46 kcal/mol
Surface area28050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.8, 128.8, 91.1
Angle α, β, γ (deg.)90.0, 90.0, 120.0
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Nodulation fucosyltransferase NodZ / NodZ alfa1 / 6-fucosyltransferase


Mass: 37828.988 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bradyrhizobium sp. (bacteria) / Strain: WM9 / Gene: nodZ / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL
References: UniProt: Q9AQ17, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.88 Å3/Da / Density % sol: 57.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 350 mM potassium sodium tartrate 100 mM MES pH 6.5 50 mM MgCl2 , VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.97242 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 24, 2011
RadiationMonochromator: double crystal Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97242 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. all: 19194 / Num. obs: 19190 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 10.6 % / Biso Wilson estimate: 56.6 Å2 / Rmerge(I) obs: 0.091 / Χ2: 1.042 / Net I/σ(I): 20.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.35-2.4310.10.6563.318780.733100
2.43-2.5310.20.4718700.812100
2.53-2.6510.20.33718720.947100
2.65-2.79100.25819021.069100
2.79-2.9610.60.18218771.089100
2.96-3.1910.90.1419041.392100
3.19-3.5110.90.11419201.115100
3.51-4.02110.10519321.168100
4.02-5.0611.60.07919551.02199.9
5.06-5010.80.04520801.02198.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
SERGUIAPS beamline softwaredata collection
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2HHC

2hhc


Resolution: 2.35→50 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.912 / WRfactor Rfree: 0.2731 / WRfactor Rwork: 0.22 / Occupancy max: 1 / Occupancy min: 0.1 / FOM work R set: 0.8283 / SU B: 11.438 / SU ML: 0.144 / SU R Cruickshank DPI: 0.2828 / SU Rfree: 0.2299 / Cross valid method: R-FREE / σ(F): 0 / ESU R Free: 0.23 / Stereochemistry target values: Engh & Huber
Details: HYDROGEN ATOMS WERE ADDED AT RIDING POSITIONS, U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2569 1030 5.4 %RANDOM
Rwork0.21 ---
all0.2124 19194 --
obs0.2124 19048 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 114.08 Å2 / Biso mean: 56 Å2 / Biso min: 32.53 Å2
Baniso -1Baniso -2Baniso -3
1--0.6 Å2-0.3 Å20 Å2
2---0.6 Å20 Å2
3---0.89 Å2
Refinement stepCycle: LAST / Resolution: 2.35→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2345 0 34 82 2461
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222495
X-RAY DIFFRACTIONr_bond_other_d0.0010.021769
X-RAY DIFFRACTIONr_angle_refined_deg1.4911.9673393
X-RAY DIFFRACTIONr_angle_other_deg0.8763.0014237
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9785297
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.44822.205127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.49315416
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0941531
X-RAY DIFFRACTIONr_chiral_restr0.0950.2367
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212749
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02561
X-RAY DIFFRACTIONr_mcbond_it0.861.51479
X-RAY DIFFRACTIONr_mcbond_other0.1691.5582
X-RAY DIFFRACTIONr_mcangle_it1.6712.52405
X-RAY DIFFRACTIONr_scbond_it4.20351016
X-RAY DIFFRACTIONr_scangle_it6.27910984
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.275 75
Rwork0.238 1294
all-1369
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.5537-0.0605-0.01914.81721.26291.45780.0696-0.12780.17850.079-0.08140.331-0.051-0.15260.01180.00520.0072-0.02980.0881-0.03050.0571.510555.77093.2123
23.1741-2.2530.78193.9414-1.34983.2928-0.052-0.2512-0.08060.28230.0289-0.03880.0953-0.02960.0230.06030.0294-0.06630.0875-0.01230.067417.802332.13583.3641
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 149
2X-RAY DIFFRACTION2A150 - 317

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