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- PDB-2hlh: Crystal structure of fucosyltransferase NodZ from Bradyrhizobium -

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Basic information

Entry
Database: PDB / ID: 2hlh
TitleCrystal structure of fucosyltransferase NodZ from Bradyrhizobium
ComponentsNodulation fucosyltransferase
KeywordsTRANSFERASE / glycosyltransferase / fucosyltransferase / NodZ / nodulation
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
PHOSPHATE ION / Nodulation fucosyltransferase NodZ
Similarity search - Component
Biological speciesBradyrhizobium sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsBrzezinski, K. / Stepkowski, T. / Panjikar, S. / Bujacz, G. / Jaskolski, M.
Citation
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.
#1: 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.
#2: 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.
#3: 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.
History
DepositionJul 7, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2007Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Aug 30, 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 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2095
Polymers37,8291
Non-polymers3804
Water4,936274
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)130.100, 130.100, 83.300
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-405-

HOH

21A-608-

HOH

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Components

#1: Protein Nodulation 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-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 274 / 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: 2.69 Å3/Da / Density % sol: 54.25 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 1.02
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 20, 2004
RadiationMonochromator: SI DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.02 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2HHC

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.
RfactorNum. reflection% reflectionSelection details
Rfree0.206 1085 3.5 %RANDOM
Rwork0.161 ---
obs0.162 30711 99.9 %-
all-30716 --
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 mean: 27.03 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å2-0.06 Å20 Å2
2---0.13 Å20 Å2
3---0.19 Å2
Refinement stepCycle: LAST / Resolution: 1.95→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2301 0 20 274 2595
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222332
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5991.9563166
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9755282
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.64421.835109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.59715373
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9071528
X-RAY DIFFRACTIONr_chiral_restr0.0910.2348
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022574
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2080.2470
X-RAY DIFFRACTIONr_nbd_other0.22245
X-RAY DIFFRACTIONr_nbtor_refined0.1850.21151
X-RAY DIFFRACTIONr_nbtor_other0.21421
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.2190
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2620.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2850.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1980.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3391.51836
X-RAY DIFFRACTIONr_mcbond_other0.2551.5570
X-RAY DIFFRACTIONr_mcangle_it1.7042.52314
X-RAY DIFFRACTIONr_scbond_it3.92951043
X-RAY DIFFRACTIONr_scangle_it5.28710852
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.216 83 -
Rwork0.165 2115 -
obs--99.91 %
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)
11.12230.0056-0.16813.54270.85511.85860.0238-0.00710.0554-0.0364-0.02980.2291-0.0479-0.04970.006-0.1919-0.0132-0.0123-0.17540.0043-0.17982.899155.2893.4422
22.6386-1.86590.97813.6308-1.20812.6310.0077-0.223-0.02060.14990.0143-0.110.0256-0.0349-0.022-0.1671-0.0138-0.0041-0.1399-0.014-0.137917.467230.56914.1137
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 1502 - 150
2X-RAY DIFFRACTION2AA151 - 317151 - 317

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