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- PDB-3siw: Crystal structure of NodZ alpha-1,6-fucosyltransferase co-crystal... -

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Basic information

Entry
Database: PDB / ID: 3siw
TitleCrystal structure of NodZ alpha-1,6-fucosyltransferase co-crystallized with GDP
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: 1.98 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

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Assembly

Deposited unit
A: Nodulation fucosyltransferase NodZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5575
Polymers37,8291
Non-polymers7284
Water3,585199
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)77,11410
Polymers75,6582
Non-polymers1,4568
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area4480 Å2
ΔGint-64 kcal/mol
Surface area27020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.9, 123.9, 95.2
Angle α, β, γ (deg.)90.0, 90.0, 120.0
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-373-

HOH

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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.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / 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: 2.79 Å3/Da / Density % sol: 55.88 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 1, 2010
RadiationMonochromator: Rosenbaum-Rock double-crystal Si(220) monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 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
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.98-2.059.40.70630031.544199.9
2.05-2.139.80.53830201.121100
2.13-2.239.90.40630201.4611100
2.23-2.35100.29930351.051100
2.35-2.49100.21430421.0381100
2.49-2.69100.15230510.9981100
2.69-2.969.90.12630840.981100
2.96-3.399.90.09930821.0111100
3.39-4.269.70.07331361.0151100
4.26-509.10.06833101.027199.3

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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: 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
RfactorNum. reflection% reflectionSelection details
Rfree0.2173 1103 3.6 %RANDOM
Rwork0.1721 ---
all0.1737 30528 --
obs0.1737 30451 99.75 %-
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: 89.07 Å2 / Biso mean: 32.892 Å2 / Biso min: 11.49 Å2
Baniso -1Baniso -2Baniso -3
1--1.4 Å2-0.7 Å20 Å2
2---1.4 Å20 Å2
3---2.1 Å2
Refinement stepCycle: LAST / Resolution: 1.98→46.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2333 0 43 199 2575
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0222546
X-RAY DIFFRACTIONr_bond_other_d0.0010.021813
X-RAY DIFFRACTIONr_angle_refined_deg1.6981.9693465
X-RAY DIFFRACTIONr_angle_other_deg0.9593.0014349
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0235300
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.17421.985131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.57515436
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1091533
X-RAY DIFFRACTIONr_chiral_restr0.1070.2375
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212773
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02575
X-RAY DIFFRACTIONr_mcbond_it1.0181.51483
X-RAY DIFFRACTIONr_mcbond_other0.2731.5581
X-RAY DIFFRACTIONr_mcangle_it1.8462.52424
X-RAY DIFFRACTIONr_scbond_it3.81951063
X-RAY DIFFRACTIONr_scangle_it5.609101034
LS refinement shellResolution: 1.98→2.031 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 86 -
Rwork0.209 2130 -
all-2216 -
obs--99.15 %
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)
11.731-0.1998-0.05163.60651.04261.67880.0489-0.11270.08280.0423-0.06730.1310.027-0.09070.01840.0133-0.0042-0.00760.0351-0.00910.02180.368954.14572.5525
22.4049-1.79410.6643.7637-1.83713.3190.0038-0.2348-0.09340.20140.0025-0.02990.0726-0.0152-0.00640.0416-0.0061-0.02250.05130.00330.020716.284730.42382.4208
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 149
2X-RAY DIFFRACTION2A150 - 318

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