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- PDB-9nj1: GlfT2 from Nocardia brasiliensis Bound to Galf Tetrasaccharide -

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Basic information

Entry
Database: PDB / ID: 9nj1
TitleGlfT2 from Nocardia brasiliensis Bound to Galf Tetrasaccharide
ComponentsGalactofuranosyltransferase
KeywordsTRANSFERASE / Glycosyltransferase / Membrane / Galactofuranose / Galactan
Function / homology
Function and homology information


glycosyltransferase activity
Similarity search - Function
Galactofuranosyltransferase GlfT2, N-terminal / Galactofuranosyltransferase-2, C-terminal / Galactofuranosyltransferase 2 N-terminal / Galactofuranosyltransferase-2, domain 3 / Glycosyltransferase like family 2 / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
: / Chem-TON / Galactofuranosyltransferase
Similarity search - Component
Biological speciesNocardia brasiliensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsCarter, A.W. / Dodge, G.J. / Kiessling, L.L.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)5R01 AI126592-09 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1F31 GM148069 United States
CitationJournal: To Be Published
Title: GlfT2 from Nocardia brasiliensis
Authors: Carter, A.W. / Dodge, G.J. / Keys, A.M. / Justen, A.M. / Taylor, K.I. / Imperiali, B. / Kulik, H.J. / Kiessling, L.L.
History
DepositionFeb 26, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Galactofuranosyltransferase
B: Galactofuranosyltransferase
C: Galactofuranosyltransferase
D: Galactofuranosyltransferase
E: Galactofuranosyltransferase
F: Galactofuranosyltransferase
G: Galactofuranosyltransferase
H: Galactofuranosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)599,23339
Polymers589,1258
Non-polymers10,10831
Water00
1
A: Galactofuranosyltransferase
C: Galactofuranosyltransferase
hetero molecules

E: Galactofuranosyltransferase
G: Galactofuranosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)299,66820
Polymers294,5634
Non-polymers5,10516
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
2
B: Galactofuranosyltransferase
D: Galactofuranosyltransferase
F: Galactofuranosyltransferase
H: Galactofuranosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)299,56519
Polymers294,5634
Non-polymers5,00315
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.210, 203.912, 292.480
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein / Sugars , 2 types, 16 molecules ABCDEFGH

#1: Protein
Galactofuranosyltransferase


Mass: 73640.633 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nocardia brasiliensis (bacteria) / Gene: O3I_000690 / Plasmid: pAMJ24 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: K0EQQ2
#2: Polysaccharide
beta-D-galactofuranose-(1-6)-beta-D-galactofuranose-(1-5)-beta-D-galactofuranose-(1-6)-beta-D-galactofuranose


Type: oligosaccharide / Mass: 666.578 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalfb1-6DGalfb1-5DGalfb1-6DGalfb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a2112h-1b_1-4]/1-1-1-1/a6-b1_b5-c1_c6-d1WURCSPDB2Glycan 1.1.0
[][<C6O4>]{[(1+1)][b-D-Galf]{[(5+1)][b-D-Galf]{[(6+1)][b-D-Galf]{}}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 23 molecules

#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-TON / 2-{2-[4-(1,1,3,3-TETRAMETHYLBUTYL)PHENOXY]ETHOXY}ETHANOL


Mass: 294.429 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C18H30O3
#5: Chemical
ChemComp-A1BYH / (2E)-12-phenoxydodec-2-en-1-ol


Mass: 276.414 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C18H28O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-TRT / FRAGMENT OF TRITON X-100 / 1-{2-[2-(2-METHOXYETHOXY)ETHOXY]ETHOXY}-4-(1,1,3,3-TETRAMETHYLBUTYL)BENZENE


Mass: 352.508 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C21H36O4 / Comment: detergent*YM

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.6 Å3/Da / Density % sol: 54.24 % / Description: Plate
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 6 mg/mL protein, 0.2% Triton X-100, 0.066 M imidazole, 2 mM magnesium chloride, 8.75% w/v PEG1000, 8.75% w/v PEG3350, 8.75% v/v MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 30, 2023
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 3.15→34.88 Å / Num. obs: 108981 / % possible obs: 98.57 % / Redundancy: 6.9 % / Biso Wilson estimate: 59.05 Å2 / Rmerge(I) obs: 0.356 / Net I/σ(I): 5.1
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsDiffraction-ID
3.15-3.261.521107011
3.26-3.391.179108821
3.39-3.550.919109171
3.55-3.730.666107571
3.73-3.970.483106641
3.97-4.270.355108911
4.27-4.70.247109751
4.7-5.380.225109841
5.38-6.770.217110781
6.77-34.880.094111321

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.15→34.88 Å / SU ML: 0.4823 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.261
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2782 3803 1.83 %
Rwork0.2381 203689 -
obs0.2388 108885 97.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.22 Å2
Refinement stepCycle: LAST / Resolution: 3.15→34.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms39036 0 547 0 39583
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011140605
X-RAY DIFFRACTIONf_angle_d0.608255307
X-RAY DIFFRACTIONf_chiral_restr0.07496179
X-RAY DIFFRACTIONf_plane_restr0.00417124
X-RAY DIFFRACTIONf_dihedral_angle_d11.088414838
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.15-3.190.37291280.3547132X-RAY DIFFRACTION92.7
3.19-3.230.38071380.33927595X-RAY DIFFRACTION98.31
3.23-3.270.37041410.33677574X-RAY DIFFRACTION98.43
3.27-3.320.36681420.32987706X-RAY DIFFRACTION98.28
3.32-3.370.35181410.31937460X-RAY DIFFRACTION98.36
3.37-3.420.31361430.32057649X-RAY DIFFRACTION98.36
3.42-3.480.38811410.30257557X-RAY DIFFRACTION98.29
3.48-3.540.30541410.2947714X-RAY DIFFRACTION98.3
3.54-3.60.33451410.28237468X-RAY DIFFRACTION98.02
3.6-3.670.31861380.27187562X-RAY DIFFRACTION97.52
3.67-3.750.2981430.27767474X-RAY DIFFRACTION97.12
3.75-3.830.32561410.26537492X-RAY DIFFRACTION96.29
3.83-3.920.28531360.25017312X-RAY DIFFRACTION94.95
3.92-4.020.29421370.23987379X-RAY DIFFRACTION96.1
4.02-4.120.29171430.23017569X-RAY DIFFRACTION98.1
4.12-4.250.25151440.22137738X-RAY DIFFRACTION99.17
4.25-4.380.24791410.21567603X-RAY DIFFRACTION99.19
4.38-4.540.27961410.19757659X-RAY DIFFRACTION99.12
4.54-4.720.25291480.19487620X-RAY DIFFRACTION99.07
4.72-4.930.21131430.19977639X-RAY DIFFRACTION98.78
4.93-5.190.24711460.20387596X-RAY DIFFRACTION98.4
5.19-5.520.23331420.2117603X-RAY DIFFRACTION98.5
5.52-5.940.30961440.2167640X-RAY DIFFRACTION98.78
5.94-6.540.22961380.21727622X-RAY DIFFRACTION98.39
6.54-7.470.24091420.20837524X-RAY DIFFRACTION97.68
7.47-9.380.19221420.16827511X-RAY DIFFRACTION97.19
9.39-34.880.21841380.18097291X-RAY DIFFRACTION94.36

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