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- PDB-4fiy: Crystal Structure of GlfT2 Complexed with UDP -

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Basic information

Entry
Database: PDB / ID: 4fiy
TitleCrystal Structure of GlfT2 Complexed with UDP
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
: / URIDINE-5'-DIPHOSPHATE / Galactofuranosyltransferase GlfT2
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 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 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_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)148,5527
Polymers147,5422
Non-polymers1,0105
Water25214
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)297,28816
Polymers295,0834
Non-polymers2,20512
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)296,92012
Polymers295,0834
Non-polymers1,8368
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)150.398, 150.398, 147.378
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-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.82 Å3/Da / Density % sol: 56.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 7% PEG 4000, 100 mM sodium acetate, 5 mM TCEP, 10% (w/v) glycerol, 0.2% Triton X-100, pH 6.5, 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: 0.922 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 18, 2008 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.922 Å / Relative weight: 1
ReflectionResolution: 3.1→40 Å / Num. all: 35241 / Num. obs: 31773 / % possible obs: 99.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 8.8 % / Biso Wilson estimate: 120 Å2 / Rmerge(I) obs: 0.125 / Rsym value: 0.125 / Net I/σ(I): 22
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 7 % / Rmerge(I) obs: 0.01 / Mean I/σ(I) obs: 1.9 / Num. unique all: 3076 / Rsym value: 0.01 / % possible all: 99.2

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHENIXmodel building
REFMAC5.5.0109refinement
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FIX

4fix


Resolution: 3.1→40 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.834 / SU B: 43.507 / SU ML: 0.353 / Cross valid method: THROUGHOUT / ESU R Free: 0.531 / Stereochemistry target values: Engh & Huber
Details: Anisotropic contribution derived from TLS domain model was added using TLSANL analysis
RfactorNum. reflection% reflectionSelection details
Rfree0.28711 1564 5.1 %RANDOM
Rwork0.2071 ---
all0.211 31299 --
obs0.211 31299 98.9 %-
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: 75.386 Å2
Baniso -1Baniso -2Baniso -3
1--1.93 Å20 Å20 Å2
2---1.93 Å20 Å2
3---3.86 Å2
Refinement stepCycle: LAST / Resolution: 3.1→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9956 0 58 14 10028
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02210283
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1291.95214023
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.70451254
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.61822.75480
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.868151630
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7091596
X-RAY DIFFRACTIONr_chiral_restr0.0750.21532
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217940
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.23926290
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.3552.510162
X-RAY DIFFRACTIONr_scbond_it3.0523.53993
X-RAY DIFFRACTIONr_scangle_it5.0874.53861
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.397 102 -
Rwork0.336 1821 -
obs-1821 85.13 %
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)
10.86030.42180.57691.20870.2541.3086-0.0864-0.05490.01220.0480.08570.16640.0002-0.15170.00070.2203-0.0154-0.01810.24660.02940.2036128.87260.48963.422
21.9426-0.25350.24421.38330.71921.59950.09990.0837-0.5020.01760.07120.17190.2516-0.0366-0.17110.2286-0.055-0.09230.1539-0.0120.2811133.46639.79651.108
35.5192-0.2976-0.5131.14030.24711.80490.25540.5944-0.7373-0.3271-0.17840.35340.26880.0151-0.07690.44180.0637-0.18620.3321-0.2710.3613141.55129.90131.952
43.2238-0.1692-0.52412.1280.82224.56790.11620.80480.1092-0.4641-0.1401-0.0188-0.3232-0.12580.02390.41560.1432-0.02190.4653-0.11040.1334158.83241.56125.058
51.06350.4652-0.42980.8003-0.5881.2297-0.03410.0775-0.0056-0.13240.0268-0.0487-0.03060.23850.00730.2355-0.0260.00990.26550.01160.137995.75115.95345.28
61.90460.08410.0371.6494-0.33491.38970.01760.13620.2723-0.16460.03240.0528-0.35450.0514-0.050.3631-0.08570.00870.17240.08150.148489.94136.41433.113
76.01591.32910.4891.635-0.58882.6724-0.07130.81450.4065-0.34550.0594-0.1381-0.520.02480.0120.6918-0.0499-0.00990.40480.31230.275281.26545.88914.009
85.61.8114-0.02782.1534-1.18022.4292-0.28761.352-0.3517-0.57260.47720.2006-0.039-0.1335-0.18960.6426-0.0079-0.1140.75620.05510.137864.70433.4046.974
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 - 628
5X-RAY DIFFRACTION4A493 - 579
6X-RAY DIFFRACTION5B1 - 157
7X-RAY DIFFRACTION6B158 - 405
8X-RAY DIFFRACTION7B406 - 492
9X-RAY DIFFRACTION7B580 - 628
10X-RAY DIFFRACTION8B493 - 579

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