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- PDB-4rif: Landomycin Glycosyltransferase LanGT2, carbasugar substrate complex -

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Basic information

Entry
Database: PDB / ID: 4rif
TitleLandomycin Glycosyltransferase LanGT2, carbasugar substrate complex
ComponentsGlycosyl transferase homolog
KeywordsTRANSFERASE / GT fold / glycosyltransferase
Function / homology
Function and homology information


UDP-glycosyltransferase activity / hexosyltransferase activity / antibiotic biosynthetic process
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
Chem-3R2 / Glycosyl transferase homolog
Similarity search - Component
Biological speciesStreptomyces cyanogenus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,8734
Polymers80,8122
Non-polymers1,0612
Water3,747208
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2970 Å2
ΔGint-14 kcal/mol
Surface area28310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.970, 59.710, 71.990
Angle α, β, γ (deg.)87.30, 73.97, 64.92
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Glycosyl transferase homolog


Mass: 40406.105 Da / Num. of mol.: 2
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: Chemical ChemComp-3R2 / 2'-deoxy-5'-O-[(R)-{[(R)-{[(1S,3R,4R,5S)-3,4-dihydroxy-5-methylcyclohexyl]oxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-3,4-dihydrothymidine


Mass: 530.357 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H28N2O13P2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 208 / 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: 2.68 Å3/Da / Density % sol: 54.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.8
Details: 1.3 M sodium citrate 0.1 M HEPES/NaOH, pH 6.8, VAPOR DIFFUSION, 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: 1.85→50.36 Å / Num. all: 71527 / Num. obs: 62872 / % possible obs: 87.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2.5 / Biso Wilson estimate: 19.28 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 7.5

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Processing

Software
NameVersionClassification
MOLREPphasing
BUSTER2.10.0refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: unliganded structure

Resolution: 1.85→50.36 Å / Cor.coef. Fo:Fc: 0.9436 / Cor.coef. Fo:Fc free: 0.9271 / SU R Cruickshank DPI: 0.131 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1982 3198 5.09 %RANDOM
Rwork0.1758 ---
all0.1769 71527 --
obs0.1769 62865 87.91 %-
Displacement parametersBiso mean: 25.23 Å2
Baniso -1Baniso -2Baniso -3
1--1.4908 Å21.2448 Å25.0073 Å2
2--2.1497 Å2-0.1843 Å2
3----0.6589 Å2
Refine analyzeLuzzati coordinate error obs: 0.201 Å
Refinement stepCycle: LAST / Resolution: 1.85→50.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5603 0 68 208 5879
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015811HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.987952HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2599SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes126HARMONIC2
X-RAY DIFFRACTIONt_gen_planes865HARMONIC5
X-RAY DIFFRACTIONt_it5811HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.3
X-RAY DIFFRACTIONt_other_torsion2.64
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion764SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6791SEMIHARMONIC4
LS refinement shellResolution: 1.85→1.9 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2367 228 4.96 %
Rwork0.1931 4372 -
all0.1951 4600 -
obs--87.91 %
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)
10.36820.0430.23080.46350.08460.51340.0309-0.0791-0.07240.0915-0.0237-0.0430.01590-0.0072-0.0094-0.016-0.0212-0.05510.0327-0.0032-0.16690.35490.3292
20.3822-0.04140.12550.5529-0.19990.0833-0.01760.00740.0495-0.12770.02710.1071-0.0001-0.0011-0.00950.0025-0.0055-0.0357-0.06790.00840.0092-14.77919.2459-23.8565
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A1 - 379
2X-RAY DIFFRACTION1{ A|* }A401
3X-RAY DIFFRACTION2{ B|* }B1 - 379
4X-RAY DIFFRACTION2{ B|* }B401

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