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- PDB-2ocx: Crystal structure of Se-Met fucosyltransferase NodZ from Bradyrhi... -

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Basic information

Entry
Database: PDB / ID: 2ocx
TitleCrystal structure of Se-Met fucosyltransferase NodZ from Bradyrhizobium
ComponentsNodulation fucosyltransferase NodZ
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 / MAD / Resolution: 2.2 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
DepositionDec 21, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Oct 18, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.3Dec 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_unobs_or_zero_occ_atoms / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)38,5645
Polymers38,1571
Non-polymers4074
Water3,243180
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)124.2, 124.2, 96.2
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-359-

HOH

21A-398-

HOH

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Components

#1: Protein Nodulation fucosyltransferase NodZ


Mass: 38157.250 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


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.82 Å3/Da / Density % sol: 56.44 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.3M potassium dihydrogen phosphate, 0.1M Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.9537, 0.9787, 0.9790
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 20, 2004
RadiationMonochromator: Si double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.95371
20.97871
30.9791
ReflectionResolution: 2.2→20 Å / Num. all: 22641 / Num. obs: 22609 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 42.6 % / Biso Wilson estimate: 35.4 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 56
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 43.1 % / Rmerge(I) obs: 0.346 / Mean I/σ(I) obs: 13.4 / Num. unique all: 2202 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
MAR345data collection
DENZOdata reduction
SCALEPACKdata scaling
Auto-Rickshawphasing
RefinementMethod to determine structure: MAD / Resolution: 2.2→19.96 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.938 / SU B: 8.947 / SU ML: 0.12 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.197 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: The refinement included TLS parameters. Residues 179-190, 245-256 and 318-330 were not modeled due to lack of electron density. There was no observed electron density for side chain atoms of ...Details: The refinement included TLS parameters. Residues 179-190, 245-256 and 318-330 were not modeled due to lack of electron density. There was no observed electron density for side chain atoms of residues 87, 102, 118, 119, 177, 178, 191, 193, 227, 258, 259, 305, 306, 307, 310. Those atoms were modeled with zero occupancy and B-factor of 70 A2.
RfactorNum. reflection% reflectionSelection details
Rfree0.217 1062 4.7 %RANDOM
Rwork0.184 ---
all0.186 22625 --
obs0.186 22498 99.47 %-
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: 32.68 Å2
Baniso -1Baniso -2Baniso -3
1--1.42 Å2-0.71 Å20 Å2
2---1.42 Å20 Å2
3---2.13 Å2
Refinement stepCycle: LAST / Resolution: 2.2→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2349 0 23 180 2552
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222423
X-RAY DIFFRACTIONr_angle_refined_deg1.5321.963290
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9355291
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.51122.155116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.57715396
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0071528
X-RAY DIFFRACTIONr_chiral_restr0.090.2359
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022669
X-RAY DIFFRACTIONr_nbd_refined0.2110.2521
X-RAY DIFFRACTIONr_nbtor_refined0.1850.21170
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2154
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1990.210
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1960.214
X-RAY DIFFRACTIONr_mcbond_it1.0041.51754
X-RAY DIFFRACTIONr_mcangle_it1.4562.52393
X-RAY DIFFRACTIONr_scbond_it4.06551061
X-RAY DIFFRACTIONr_scangle_it5.57110897
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 84 -
Rwork0.223 1519 -
obs-1603 99.26 %
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)
11.519-0.2017-0.17073.6049-0.981.58950.0378-0.0868-0.09470.0905-0.0546-0.1882-0.01610.04810.0168-0.17590.00330.0375-0.11480.0092-0.1582-0.396-54.19912.1647
23.6702-2.3207-1.29344.03721.71093.0038-0.0423-0.29310.12580.21430.0714-0.0147-0.06550.1145-0.0292-0.12380.02350.0389-0.08330.0126-0.1169-16.6828-30.64732.6332
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDAuth seq-IDLabel seq-ID
112 - 1502 - 150
22151 - 317151 - 317

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