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- PDB-9dtp: GlfT2 from Nocardia brasiliensis -

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Basic information

Entry
Database: PDB / ID: 9dtp
TitleGlfT2 from Nocardia brasiliensis
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: 3.11 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
DepositionOct 1, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 8, 2025Provider: 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)593,52139
Polymers589,1258
Non-polymers4,39631
Water00
1
A: Galactofuranosyltransferase
D: Galactofuranosyltransferase
F: Galactofuranosyltransferase
G: Galactofuranosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)296,71419
Polymers294,5634
Non-polymers2,15215
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Galactofuranosyltransferase
C: Galactofuranosyltransferase
hetero molecules

E: Galactofuranosyltransferase
H: Galactofuranosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)296,80720
Polymers294,5634
Non-polymers2,24416
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Unit cell
Length a, b, c (Å)107.026, 205.045, 295.320
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: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#3: 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
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C3H8O3
Has ligand of interestN
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: 54.5 % / 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: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 10, 2021
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 3.11→20.05 Å / Num. obs: 112050 / % possible obs: 96.01 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.26 / Net I/σ(I): 4.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsDiffraction-ID% possible all
3.11-3.224.451.354111431199.02
3.22-3.354.621.0461.411575199.97
3.35-3.50.8211.67039161.14
3.5-3.694.50.5632.611587199.92
3.69-3.924.350.4143.411570199.95
3.92-4.224.490.2874.711605199.92
4.22-4.634.660.1866.711680199.95
4.63-5.294.490.1657.211691199.88
5.29-6.634.310.1766.611778199.92
6.63-20.054.340.07512.512094199.9

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
JBluIce-EPICSdata collection
XDS20230630data reduction
XDS20230630data scaling
PHENIX1.21.2_5419phasing
Coot0.9.8.95model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.11→20.05 Å / SU ML: 0.4479 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.0514
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2575 3797 1.78 %
Rwork0.2209 209134 -
obs0.2216 111965 94.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.72 Å2
Refinement stepCycle: LAST / Resolution: 3.11→20.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms38996 0 262 0 39258
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001540275
X-RAY DIFFRACTIONf_angle_d0.433654824
X-RAY DIFFRACTIONf_chiral_restr0.046040
X-RAY DIFFRACTIONf_plane_restr0.00427117
X-RAY DIFFRACTIONf_dihedral_angle_d10.589614671
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.11-3.150.36141380.33897601X-RAY DIFFRACTION92.14
3.15-3.190.33931470.32648000X-RAY DIFFRACTION98.82
3.19-3.240.41181470.33688127X-RAY DIFFRACTION98.92
3.24-3.280.39781470.33238036X-RAY DIFFRACTION99.33
3.28-3.330.36681530.33038127X-RAY DIFFRACTION99.39
3.33-3.380.3361490.30998108X-RAY DIFFRACTION99.4
3.38-3.430.39351100.31556013X-RAY DIFFRACTION94.53
3.48-3.50.3499280.30811536X-RAY DIFFRACTION84.22
3.5-3.560.32581460.28868092X-RAY DIFFRACTION98.45
3.56-3.630.28951460.26518011X-RAY DIFFRACTION98.75
3.63-3.70.30451450.25928136X-RAY DIFFRACTION99.15
3.7-3.780.32421430.25978012X-RAY DIFFRACTION98.92
3.78-3.870.24221420.24968067X-RAY DIFFRACTION98.58
3.87-3.960.29031440.23888084X-RAY DIFFRACTION98.48
3.96-4.070.24711460.2237900X-RAY DIFFRACTION97.3
4.07-4.190.27081490.20998169X-RAY DIFFRACTION99.74
4.19-4.320.26791460.19858090X-RAY DIFFRACTION99.82
4.32-4.480.21111520.18798191X-RAY DIFFRACTION99.64
4.48-4.650.23961460.178145X-RAY DIFFRACTION99.52
4.65-4.860.21181470.17728164X-RAY DIFFRACTION99.59
4.86-5.110.22751440.18348065X-RAY DIFFRACTION99.11
5.12-5.430.24671460.20277993X-RAY DIFFRACTION98.19
5.43-5.840.24931440.20968051X-RAY DIFFRACTION99.07
5.84-6.410.19921490.2088057X-RAY DIFFRACTION98.3
6.41-7.30.26131420.19938158X-RAY DIFFRACTION99.92
7.3-9.050.15721520.15318135X-RAY DIFFRACTION99.75
9.05-20.050.1681490.1418066X-RAY DIFFRACTION98.79

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