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- PDB-9nj0: GlfT2 from Nocardia brasiliensis Bound to Galf Trisaccharide -

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Basic information

Entry
Database: PDB / ID: 9nj0
TitleGlfT2 from Nocardia brasiliensis Bound to Galf Trisaccharide
ComponentsGalactofuranosyltransferase
KeywordsTRANSFERASE / Glycosyltransferase / Membrane / Galactofuranose / Galactan
Function / homologyGalactofuranosyltransferase GlfT2, N-terminal / Galactofuranosyltransferase-2, C-terminal / Galactofuranosyltransferase 2 N-terminal / Galactofuranosyltransferase-2, domain 3 / Glycosyltransferase like family 2 / glycosyltransferase activity / Nucleotide-diphospho-sugar transferases / : / Galactofuranosyltransferase
Function and homology information
Biological speciesNocardia brasiliensis ATCC 700358 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 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)598,38640
Polymers589,1258
Non-polymers9,26132
Water00
1
C: Galactofuranosyltransferase
H: Galactofuranosyltransferase
hetero molecules

A: Galactofuranosyltransferase
F: Galactofuranosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)299,19320
Polymers294,5634
Non-polymers4,63116
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
2
B: Galactofuranosyltransferase
D: Galactofuranosyltransferase
E: Galactofuranosyltransferase
G: Galactofuranosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)299,19320
Polymers294,5634
Non-polymers4,63116
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.784, 204.965, 294.126
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

#1: Protein
Galactofuranosyltransferase / GlfT2


Mass: 73640.633 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nocardia brasiliensis ATCC 700358 (bacteria)
Strain: HUJEG-1 / Gene: O3I_000690 / Plasmid: pAMJ24 / Details (production host): pET28a-His6-NbrGlfT2 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5a / References: UniProt: K0EQQ2
#2: Polysaccharide
beta-D-galactofuranose-(1-5)-beta-D-galactofuranose-(1-6)-beta-D-galactofuranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 8 / Source method: obtained synthetically
DescriptorTypeProgram
DGalfb1-5DGalfb1-6DGalfb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2112h-1b_1-4]/1-1-1/a6-b1_b5-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Galf]{[(6+1)][b-D-Galf]{[(5+1)][b-D-Galf]{}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#4: 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.: 8 / Source method: obtained synthetically / Formula: C21H36O4 / Comment: detergent*YM
#5: Chemical
ChemComp-A1BYH / (2E)-12-phenoxydodec-2-en-1-ol


Mass: 276.414 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C18H28O2 / Feature type: SUBJECT OF INVESTIGATION
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: 2.7 Å3/Da / Density % sol: 54.2 % / Description: Plate
Crystal growTemperature: 293.15 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: 3.2→34.61 Å / Num. obs: 101657 / % possible obs: 94.9 % / Redundancy: 5.2 % / Rpim(I) all: 0.135 / Net I/σ(I): 5.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2Rpim(I) all% possible all
3.2-3.315.271.6100210.890.43594.73
3.31-3.455.28102340.780.37596.33
3.45-3.62.5101350.610.29395.83
3.6-3.795.13101840.4980.2495.8
3.79-4.034.743.9101120.3850.1995.2
4.03-4.345.345.3101190.2810.13494.91
4.34-4.785.297.1101690.1970.09494.98
4.78-5.465.037.2101680.1890.09294.63
5.46-6.885.77.6102090.1770.08594.14
6.88-34.615.4714.6103210.0790.03892.27

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDS20230630data reduction
XDS20230630data scaling
PHENIX1.21.2_5419phasing
Coot0.9.6model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→34.61 Å / SU ML: 0.4425 / Cross valid method: FREE R-VALUE / Phase error: 24.4682
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.248 -1.97 %
Rwork0.1997 185755 -
obs0.2006 101657 92.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.81 Å2
Refinement stepCycle: LAST / Resolution: 3.2→34.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms39120 0 459 0 39579
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002840635
X-RAY DIFFRACTIONf_angle_d0.60755347
X-RAY DIFFRACTIONf_chiral_restr0.04276160
X-RAY DIFFRACTIONf_plane_restr0.00467152
X-RAY DIFFRACTIONf_dihedral_angle_d12.239814844
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.240.36731300.30936498X-RAY DIFFRACTION87.29
3.24-3.280.36651410.30296937X-RAY DIFFRACTION92.63
3.28-3.330.34471390.29476954X-RAY DIFFRACTION92.73
3.33-3.370.35181390.28256872X-RAY DIFFRACTION92.82
3.37-3.420.32761340.27826969X-RAY DIFFRACTION92.67
3.42-3.480.31941350.27236920X-RAY DIFFRACTION92.67
3.48-3.540.30741400.25436985X-RAY DIFFRACTION92.75
3.54-3.60.31451380.25296877X-RAY DIFFRACTION92.58
3.6-3.660.30761410.25136914X-RAY DIFFRACTION92.29
3.66-3.730.28951400.23816827X-RAY DIFFRACTION91.93
3.73-3.810.31091390.23086902X-RAY DIFFRACTION92.02
3.81-3.890.28771360.21666790X-RAY DIFFRACTION91.94
3.89-3.980.23081420.20786883X-RAY DIFFRACTION91.48
3.98-4.080.2281370.19866890X-RAY DIFFRACTION91.84
4.08-4.190.24021350.18646828X-RAY DIFFRACTION91.78
4.19-4.310.21491330.18186856X-RAY DIFFRACTION91.78
4.31-4.450.20661400.16476930X-RAY DIFFRACTION91.66
4.45-4.610.24471410.15386809X-RAY DIFFRACTION91.92
4.61-4.80.19541380.15756916X-RAY DIFFRACTION92.43
4.8-5.010.22141430.16036890X-RAY DIFFRACTION92.58
5.01-5.280.18311430.16816973X-RAY DIFFRACTION93.1
5.28-5.610.22051420.16786965X-RAY DIFFRACTION93.01
5.61-6.040.21981430.17786927X-RAY DIFFRACTION93.01
6.04-6.640.24481420.17826921X-RAY DIFFRACTION92.81
6.64-7.590.16621410.16616928X-RAY DIFFRACTION92.57
7.59-9.530.15711330.13636859X-RAY DIFFRACTION91.9
9.53-34.610.22971320.15746735X-RAY DIFFRACTION90.05

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