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- PDB-4fix: Crystal Structure of GlfT2 -

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Basic information

Entry
Database: PDB / ID: 4fix
TitleCrystal Structure of GlfT2
ComponentsUDP-galactofuranosyl transferase GlfT2
KeywordsTRANSFERASE / Galactofuranosyltransferase / CAZY GT-2 family / Glycosyltransferase / Carbohydrate binding / Membrane
Function / homology
Function and homology information


galactofuranosylgalactofuranosylrhamnosyl-N-acetylglucosaminyl-diphospho-decaprenol beta-1,5/1,6-galactofuranosyltransferase / lipopolysaccharide-1,6-galactosyltransferase activity / lipopolysaccharide-1,5-galactosyltransferase activity / UDP-D-galactose metabolic process / cell wall macromolecule biosynthetic process / cell wall polysaccharide biosynthetic process / UDP-galactosyltransferase activity / mycolate cell wall layer assembly / capsule polysaccharide biosynthetic process / lipopolysaccharide biosynthetic process ...galactofuranosylgalactofuranosylrhamnosyl-N-acetylglucosaminyl-diphospho-decaprenol beta-1,5/1,6-galactofuranosyltransferase / lipopolysaccharide-1,6-galactosyltransferase activity / lipopolysaccharide-1,5-galactosyltransferase activity / UDP-D-galactose metabolic process / cell wall macromolecule biosynthetic process / cell wall polysaccharide biosynthetic process / UDP-galactosyltransferase activity / mycolate cell wall layer assembly / capsule polysaccharide biosynthetic process / lipopolysaccharide biosynthetic process / glycosyltransferase activity / cell wall organization / transferase activity / metal ion binding / plasma membrane / cytosol
Similarity search - Function
Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A - #60 / Galactofuranosyltransferase GlfT2, N-terminal / Galactofuranosyltransferase-2, C-terminal / Galactofuranosyltransferase 2 N-terminal / Galactofuranosyltransferase-2, domain 3 / Glycosyltransferase like family 2 / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / : / Galactofuranosyltransferase GlfT2
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.45 Å
AuthorsWheatley, R.W. / Zheng, R.B. / Lowary, T.L. / Ng, K.K.S.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Tetrameric Structure of the GlfT2 Galactofuranosyltransferase Reveals a Scaffold for the Assembly of Mycobacterial Arabinogalactan.
Authors: Wheatley, R.W. / Zheng, R.B. / Richards, M.R. / Lowary, T.L. / Ng, K.K.
History
DepositionJun 11, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2012Group: Database references
Revision 1.2Oct 17, 2012Group: Derived calculations
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _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

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Assembly

Deposited unit
A: UDP-galactofuranosyl transferase GlfT2
B: UDP-galactofuranosyl transferase GlfT2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,0989
Polymers147,5422
Non-polymers5567
Water7,422412
1
A: UDP-galactofuranosyl transferase GlfT2
hetero molecules

A: UDP-galactofuranosyl transferase GlfT2
hetero molecules

A: UDP-galactofuranosyl transferase GlfT2
hetero molecules

A: UDP-galactofuranosyl transferase GlfT2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)296,40820
Polymers295,0834
Non-polymers1,32516
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-x+2,-y+1,z1
crystal symmetry operation3_645-y+3/2,x-1/2,z1
crystal symmetry operation4_565y+1/2,-x+3/2,z1
2
B: UDP-galactofuranosyl transferase GlfT2
hetero molecules

B: UDP-galactofuranosyl transferase GlfT2
hetero molecules

B: UDP-galactofuranosyl transferase GlfT2
hetero molecules

B: UDP-galactofuranosyl transferase GlfT2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)295,98416
Polymers295,0834
Non-polymers90112
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_545-y+1/2,x-1/2,z1
crystal symmetry operation4_555y+1/2,-x+1/2,z1
Unit cell
Length a, b, c (Å)150.791, 150.791, 148.016
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212

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Components

#1: Protein UDP-galactofuranosyl transferase GlfT2 / GalTr / Beta-D-(1-5)galactofuranosyltransferase / Beta-D-(1-6)galactofuranosyltransferase / UDP- ...GalTr / Beta-D-(1-5)galactofuranosyltransferase / Beta-D-(1-6)galactofuranosyltransferase / UDP-Galf:alpha-3-L-rhamnosyl-alpha-D-GlcNAc-pyrophosphate polyprenol / UDP-galactofuranosyl transferase


Mass: 73770.805 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: glfT2, Rv3808c, RV38308c / Plasmid: pET-15B / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3)
References: UniProt: O53585, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 412 / 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: 2.85 Å3/Da / Density % sol: 56.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 7% (w/v) PEG 4000, 100 mM sodium cacodylate pH 6.5, 100 mM sodium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.0442 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 18, 2008 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0442 Å / Relative weight: 1
ReflectionResolution: 2.45→40 Å / Num. all: 59863 / Num. obs: 59863 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 11.9 % / Biso Wilson estimate: 56.2 Å2 / Rmerge(I) obs: 0.104 / Rsym value: 0.104 / Net I/σ(I): 27.2
Reflection shellResolution: 2.45→2.54 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.942 / Mean I/σ(I) obs: 2 / Num. unique all: 6192 / Rsym value: 0.942 / % possible all: 99.4

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHENIXmodel building
REFMAC5.5.0109refinement
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.45→40 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.939 / SU B: 15.503 / SU ML: 0.162
Isotropic thermal model: isotropic atomic model plus TLS anisotropic model for domains
Cross valid method: THROUGHOUT / ESU R: 0.348 / ESU R Free: 0.231 / Stereochemistry target values: Engh & Huber
Details: TLSANL was used to determine the TLS-anisotropic components of temperature factors for all atoms as obtained by refining TLS parameters for individual domains
RfactorNum. reflection% reflectionSelection details
Rfree0.22228 3195 5.1 %RANDOM
Rwork0.18463 ---
all0.18657 59863 --
obs0.18657 59863 99.92 %-
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: 56.18 Å2
Baniso -1Baniso -2Baniso -3
1--1.45 Å20 Å20 Å2
2---1.45 Å20 Å2
3---2.91 Å2
Refinement stepCycle: LAST / Resolution: 2.45→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9966 0 30 412 10408
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02210259
X-RAY DIFFRACTIONr_angle_refined_deg1.0541.94713974
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5251256
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.22922.75480
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.935151630
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4741596
X-RAY DIFFRACTIONr_chiral_restr0.0730.21526
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0217930
X-RAY DIFFRACTIONr_mcbond_it1.28926300
X-RAY DIFFRACTIONr_mcangle_it2.2312.510176
X-RAY DIFFRACTIONr_scbond_it3.2453.53959
X-RAY DIFFRACTIONr_scangle_it4.9364.53798
LS refinement shellResolution: 2.451→2.514 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 229 -
Rwork0.243 4345 -
obs-4345 99.22 %
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)
10.74430.03730.43610.87110.36971.0093-0.0306-0.1162-0.04170.04730.05350.11720.0302-0.1265-0.02290.0475-0.0189-0.00010.06830.03460.0525129.0662.99464.733
21.4639-0.24940.20171.4120.27370.95480.0773-0.083-0.45980.00040.05380.12620.18880.0018-0.13120.0762-0.0268-0.06490.02380.03740.1853132.63740.26753.361
35.3312-0.1934-1.79110.33150.01812.21630.23580.6595-0.6651-0.2604-0.20150.2730.2806-0.0397-0.03430.34420.1365-0.24020.2259-0.25330.3521140.26530.8331.001
43.00950.02921.08251.64321.81963.44810.20170.54170.0349-0.3912-0.10960.0726-0.28260.1464-0.09220.16830.1001-0.03310.178-0.06050.0778164.13943.34129.273
50.71250.318-0.20720.7567-0.48651.1419-0.0407-0.05420.00890.0136-0.0295-0.0305-0.04310.17170.07020.0453-0.01750.00890.07510.01020.037296.35113.36946.687
61.12950.1413-0.1111.3083-0.27111.3887-0.01210.06350.2067-0.03180.01310.0489-0.32470.0343-0.00110.1515-0.0459-0.01840.0410.04040.068991.90736.06535.44
74.84480.43921.16520.7142-0.57982.5484-0.11520.75860.3382-0.20160.0276-0.0395-0.3175-0.05270.08760.424-0.0267-0.02390.28380.18050.162983.8645.213.047
83.95591.3164-0.40312.7852-0.55254.0617-0.21450.995-0.1437-0.38180.28670.14380.1356-0.0979-0.07220.28990.0145-0.07620.39310.00870.06860.60331.46111.205
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 157
2X-RAY DIFFRACTION2A158 - 405
3X-RAY DIFFRACTION3A406 - 492
4X-RAY DIFFRACTION3A580 - 629
5X-RAY DIFFRACTION4A493 - 579
6X-RAY DIFFRACTION5B1 - 157
7X-RAY DIFFRACTION6B158 - 405
8X-RAY DIFFRACTION7B406 - 492
9X-RAY DIFFRACTION7B580 - 629
10X-RAY DIFFRACTION8B493 - 579

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