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- PDB-4rii: Chimeric Glycosyltransferase LanGT2S8Ac, TDP complex -

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Basic information

Entry
Database: PDB / ID: 4rii
TitleChimeric Glycosyltransferase LanGT2S8Ac, TDP complex
ComponentsGlycosyl transferase homolog,Glycosyl transferase
KeywordsTRANSFERASE / GT fold / C-glycosylating glycosyltransferase
Function / homology
Function and homology information


UDP-glycosyltransferase activity / hexosyltransferase activity / antibiotic biosynthetic process
Similarity search - Function
Erythromycin biosynthesis protein CIII-like, central / Protein of unknown function (DUF1205) / UDP-glucuronosyl/UDP-glucosyltransferase / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
THYMIDINE-5'-DIPHOSPHATE / Glycosyl transferase / Glycosyl transferase homolog
Similarity search - Component
Biological speciesStreptomyces cyanogenus (bacteria)
Streptomyces fradiae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 1.2Jun 21, 2017Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_src_gen / struct_ref_seq_dif
Item: _entity.pdbx_description / _struct_ref_seq_dif.details
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycosyl transferase homolog,Glycosyl transferase
B: Glycosyl transferase homolog,Glycosyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,7355
Polymers80,9062
Non-polymers8293
Water3,729207
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4710 Å2
ΔGint-43 kcal/mol
Surface area27260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.693, 58.669, 63.660
Angle α, β, γ (deg.)78.78, 70.16, 86.77
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A1 - 374
2010B1 - 374

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Components

#1: Protein Glycosyl transferase homolog,Glycosyl transferase


Mass: 40453.156 Da / Num. of mol.: 2 / Mutation: S8A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces cyanogenus (bacteria), (gene. exp.) Streptomyces fradiae (bacteria)
Gene: lanGT2, urdGT2 / Plasmid: pET21::langt2S8Ac / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q9ZGC0, UniProt: Q9RPA7
#2: Chemical ChemComp-TYD / THYMIDINE-5'-DIPHOSPHATE / Thymidine diphosphate


Mass: 402.188 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N2O11P2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 2.24 Å3/Da / Density % sol: 45.19 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 34% PEG 3350 0.17 M MgCl2 16 mM L-proline 0.1 M HEPES/NaOH, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 278K

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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→46.37 Å / Num. all: 47043 / Num. obs: 44926 / % possible obs: 95.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2.5 / Rmerge(I) obs: 0.047 / Net I/σ(I): 11.8

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.7.0032refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: LanGT2, wild type

Resolution: 2→46.37 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.932 / SU B: 8.469 / SU ML: 0.121 / Cross valid method: THROUGHOUT / ESU R: 0.213 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23122 2264 5 %RANDOM
Rwork0.19722 ---
all0.19896 47043 --
obs0.19896 42662 94.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.354 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20.66 Å2-1.16 Å2
2---1.67 Å2-0.98 Å2
3---0.9 Å2
Refinement stepCycle: LAST / Resolution: 2→46.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5295 0 51 207 5553
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0195470
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1821.9847493
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0475705
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.52123.378222
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.38415795
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0851547
X-RAY DIFFRACTIONr_chiral_restr0.080.2854
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0224218
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_it0.8432.0012835
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.4982.9933535
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.9062.1272635
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined4.20417.1838298
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 383 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 143 -
Rwork0.291 2857 -
obs--84.94 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.3562-0.0654-0.34881.83070.02061.0330.05420.180.0566-0.2248-0.07180.3543-0.0174-0.22660.01750.03440.0128-0.03090.0709-0.00240.1145-10.806511.9266-8.6239
20.7415-0.39380.16052.15540.64811.1547-0.0595-0.1484-0.1230.35490.0311-0.10180.234-0.08410.02840.0789-0.0065-0.00470.05890.02190.07458.1243-11.61366.9181
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 374
2X-RAY DIFFRACTION1A401 - 402
3X-RAY DIFFRACTION2B1 - 374
4X-RAY DIFFRACTION2B401

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