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- PDB-4rie: Landomycin Glycosyltransferase LanGT2 -

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Basic information

Entry
Database: PDB / ID: 4rie
TitleLandomycin Glycosyltransferase LanGT2
ComponentsGlycosyl transferase homolog
KeywordsTRANSFERASE / GT fold / glycosyltransferase
Function / homology
Function and homology information


UDP-glycosyltransferase activity / hexosyltransferase activity / antibiotic biosynthetic process / metal ion binding
Similarity search - Function
: / Erythromycin biosynthesis protein CIII-like, N-terminal domain / Erythromycin biosynthesis protein CIII-like, central / : / Erythromycin biosynthesis protein CIII-like, C-terminal domain / UDP-glucuronosyl/UDP-glucosyltransferase / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Glycosyl transferase homolog
Similarity search - Component
Biological speciesStreptomyces cyanogenus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.162 Å
AuthorsTam, H.K. / Gerhardt, S. / Breit, B. / Bechthold, A. / Einsle, O.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2015
Title: Structural Characterization of O- and C-Glycosylating Variants of the Landomycin Glycosyltransferase LanGT2.
Authors: Tam, H.K. / Harle, J. / Gerhardt, S. / Rohr, J. / Wang, G. / Thorson, J.S. / Bigot, A. / Lutterbeck, M. / Seiche, W. / Breit, B. / Bechthold, A. / Einsle, O.
History
DepositionOct 6, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 28, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycosyl transferase homolog
B: Glycosyl transferase homolog


Theoretical massNumber of molelcules
Total (without water)80,8122
Polymers80,8122
Non-polymers00
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-11 kcal/mol
Surface area30040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.992, 75.992, 214.314
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.974766, 0.024537, 0.221875), (-0.012695, -0.998425, 0.054644), (0.222866, 0.050448, 0.973543)81.23628, -5.05446, -8.98731

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Components

#1: Protein Glycosyl transferase homolog


Mass: 40406.105 Da / Num. of mol.: 2 / Fragment: Glycosyltransferase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces cyanogenus (bacteria) / Strain: S136 / Gene: lanGT2 / Plasmid: pET21::langt2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q9ZGC0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 2.21 Å3/Da / Density % sol: 44.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 1.3 M sodium citrate 0.1 M HEPES/NaOH, pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 27, 2013
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.16→214.31 Å / Num. all: 37364 / Num. obs: 37364 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2.5 / Rmerge(I) obs: 0.043 / Net I/σ(I): 40.4
Reflection shellResolution: 2.16→2.28 Å / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 5.3 / % possible all: 100

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.7.0032refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2P6P

2p6p


Resolution: 2.162→65.81 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.926 / SU B: 12.692 / SU ML: 0.16 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.272 / ESU R Free: 0.208 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24198 1859 5 %RANDOM
Rwork0.19755 ---
all0.19975 37364 --
obs0.19975 35420 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.688 Å2
Baniso -1Baniso -2Baniso -3
1-0.42 Å20.42 Å20 Å2
2--0.42 Å2-0 Å2
3----1.35 Å2
Refinement stepCycle: LAST / Resolution: 2.162→65.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5273 0 0 131 5404
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0195391
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3341.9737369
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0415700
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.73723.116215
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.34315788
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1481547
X-RAY DIFFRACTIONr_chiral_restr0.0860.2846
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0224151
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_it1.3682.5872827
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.2583.8673518
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.5862.7672564
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined5.51824.41522859
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.162→2.218 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 124 -
Rwork0.261 2599 -
obs--100 %
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)
11.33440.1389-0.1071.69550.0671.21450.0883-0.12650.22720.0917-0.11590.2333-0.3290.03120.02760.0981-0.02150.01590.1853-0.07450.075832.293811.7260.559
20.5503-0.2038-0.31461.7201-0.13850.75330.05410.0392-0.1714-0.0519-0.1306-0.26890.15780.24280.07650.10460.0287-0.02560.2542-0.0390.133449.4211-17.5002-0.8353
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 378
2X-RAY DIFFRACTION2B1 - 378

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