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- PDB-2p6p: X-ray crystal structure of C-C bond-forming dTDP-D-Olivose-transf... -

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Basic information

Entry
Database: PDB / ID: 2p6p
TitleX-ray crystal structure of C-C bond-forming dTDP-D-Olivose-transferase UrdGT2
ComponentsGlycosyl transferase
KeywordsTRANSFERASE / C-glycosyltransferase / dTDP-D-Olivose-transferase / polyketide aglycon / GT-B family / X-ray-diffraction / UrdamycinA-biosynthesis
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
Glycosyl transferase
Similarity search - Component
Biological speciesStreptomyces fradiae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.88 Å
AuthorsMittler, M. / Bechthold, A. / Schulz, G.E.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Structure and action of the C-C bond-forming glycosyltransferase UrdGT2 involved in the biosynthesis of the antibiotic urdamycin.
Authors: Mittler, M. / Bechthold, A. / Schulz, G.E.
History
DepositionMar 19, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999SEQUENCE Author states that the sequence database reference that was used for this entry (UNP ...SEQUENCE Author states that the sequence database reference that was used for this entry (UNP Q9RPA7) does not match sequence. The DB ref was removed.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)83,4639
Polymers82,8192
Non-polymers6457
Water7,440413
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.872, 78.904, 133.958
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Glycosyl transferase


Mass: 41409.289 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces fradiae (bacteria) / Strain: Streptomyces fradiae Tue2717 / Gene: urdGT2 / Plasmid: pRSET / Production host: Escherichia coli (E. coli) / Strain (production host): E. coli BL21 (DE3) pLysS / References: UniProt: Q9RPA7
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 413 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 0.1M HEPES,18% PEG 1500, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSLS X06SA11.1036
SYNCHROTRONSLS X06SA21.0377, 1.0398, 0.8551
Detector
TypeIDDetectorDate
MARMOSAIC 225 mm CCD1CCDFeb 25, 2006
MARMOSAIC 225 mm CCD2CCDFeb 13, 2005
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111 double-crystalSINGLE WAVELENGTHMx-ray1
2Si 111 double-crystalMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.10361
21.03771
31.03981
40.85511
ReflectionResolution: 1.88→68.04 Å / Num. all: 57551 / Num. obs: 57345 / % possible obs: 99.6 % / Redundancy: 4.8 % / Biso Wilson estimate: 29.84 Å2 / Rmerge(I) obs: 0.093 / Rsym value: 6.4 / Net I/σ(I): 15.7
Reflection shellResolution: 1.9→68 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 15.7 / Num. unique all: 57346 / Rsym value: 6.4 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SLS-X06SAdata collection
XDSdata reduction
XSCALEdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.88→68.04 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.933 / SU B: 7.507 / SU ML: 0.112 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.165 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22978 2868 5 %RANDOM
Rwork0.18823 ---
obs0.19028 54481 99.65 %-
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: 30.096 Å2
Baniso -1Baniso -2Baniso -3
1-0.99 Å20 Å20 Å2
2---0.21 Å20 Å2
3----0.78 Å2
Refinement stepCycle: LAST / Resolution: 1.88→68.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5734 0 42 413 6189
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0225931
X-RAY DIFFRACTIONr_angle_refined_deg1.5841.9718105
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6045761
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.65122.114246
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.66415888
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8971564
X-RAY DIFFRACTIONr_chiral_restr0.120.2930
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024556
X-RAY DIFFRACTIONr_nbd_refined0.230.22891
X-RAY DIFFRACTIONr_nbtor_refined0.3060.24012
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2403
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2530.2109
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2330.220
X-RAY DIFFRACTIONr_mcbond_it0.9041.53919
X-RAY DIFFRACTIONr_mcangle_it1.38326143
X-RAY DIFFRACTIONr_scbond_it2.2732252
X-RAY DIFFRACTIONr_scangle_it3.5314.51959
LS refinement shellResolution: 1.88→1.929 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 209 -
Rwork0.28 3962 -
obs--99.88 %
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)
11.47960.0724-0.07651.2733-0.50671.33190.05640.0990.0026-0.0633-0.0821-0.1026-0.04880.04080.0257-0.1320.0217-0.0033-0.1636-0.0258-0.16841.02334.32158.34
21.4301-0.57040.03514.5905-0.95331.63180.0883-0.0940.41510.5551-0.087-0.0437-0.48180.0188-0.0013-0.0101-0.02040.0309-0.0671-0.0379-0.072122.66949.40863.477
31.256-0.7628-1.0881.89730.8062.9214-0.0121-0.28360.00740.22480.0351-0.0848-0.12110.1238-0.023-0.1042-0.0294-0.0057-0.083-0.0028-0.100224.84934.80295.757
43.2072-0.4180.97840.5721-0.29751.4502-0.0483-0.31410.27120.1445-0.0041-0.0485-0.1120.11970.0525-0.0633-0.00330.0079-0.0705-0.039-0.116546.6224.88291.919
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1961 - 196
2X-RAY DIFFRACTION2AA197 - 382197 - 382
3X-RAY DIFFRACTION3BB1 - 1961 - 196
4X-RAY DIFFRACTION4BB197 - 383197 - 383

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