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- PDB-7erx: Glycosyltransferase in complex with UDP and STB -

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Basic information

Entry
Database: PDB / ID: 7erx
TitleGlycosyltransferase in complex with UDP and STB
ComponentsGlycosyltransferase
KeywordsTRANSFERASE / glycosyltransferase in steviol glucosylation
Function / homology
Function and homology information


UDP-glucosyltransferase activity / Transferases; Glycosyltransferases; Hexosyltransferases / nucleotide binding
Similarity search - Function
: / UDP-glycosyltransferase family, conserved site / UDP-glycosyltransferases signature. / UDP-glucoronosyl and UDP-glucosyl transferase / UDP-glucuronosyl/UDP-glucosyltransferase
Similarity search - Domain/homology
Steviolbioside / URIDINE-5'-DIPHOSPHATE / Glycosyltransferase
Similarity search - Component
Biological speciesOryza sativa subsp. japonica (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsZhu, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)31771910 China
CitationJournal: Nat Commun / Year: 2021
Title: Catalytic flexibility of rice glycosyltransferase OsUGT91C1 for the production of palatable steviol glycosides.
Authors: Zhang, J. / Tang, M. / Chen, Y. / Ke, D. / Zhou, J. / Xu, X. / Yang, W. / He, J. / Dong, H. / Wei, Y. / Naismith, J.H. / Lin, Y. / Zhu, X. / Cheng, W.
History
DepositionMay 8, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 8, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 15, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1814
Polymers51,0421
Non-polymers1,1393
Water1,53185
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint-13 kcal/mol
Surface area16160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.482, 83.173, 109.391
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Glycosyltransferase


Mass: 51042.496 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa subsp. japonica (Japanese rice)
Gene: Os03g0702000, OSNPB_030702000 / Production host: Escherichia coli (E. coli)
References: UniProt: Q0DPB7, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#4: Chemical ChemComp-JC6 / Steviolbioside


Mass: 642.732 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H50O13 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.48 Å3/Da / Density % sol: 50.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 100 mM HEPES-NaOH buffer pH 6.5 and 20% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 27, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.92→109.39 Å / Num. obs: 38620 / % possible obs: 99.7 % / Redundancy: 6.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.036 / Rrim(I) all: 0.066 / Net I/σ(I): 14.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
9.01-109.395.20.0134520.9990.0080.016
1.92-1.975.11.85224550.6261.2822.264

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Cootmodel building
DIALS0.7.4data reduction
PHASERphasing
DIALSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7ERY

7ery


Resolution: 1.92→66.297 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.958 / SU B: 9.875 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.138 / ESU R Free: 0.125
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2135 1952 5.063 %
Rwork0.1885 36603 -
all0.19 --
obs-38555 99.564 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 48.917 Å2
Baniso -1Baniso -2Baniso -3
1-4.769 Å20 Å20 Å2
2---1.981 Å20 Å2
3----2.788 Å2
Refinement stepCycle: LAST / Resolution: 1.92→66.297 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3089 0 76 85 3250
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0133284
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173146
X-RAY DIFFRACTIONr_angle_refined_deg1.4771.6474485
X-RAY DIFFRACTIONr_angle_other_deg1.2831.5747240
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8455411
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.95819.878164
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg3.456101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.02715513
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9711531
X-RAY DIFFRACTIONr_chiral_restr0.0710.2427
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023650
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02744
X-RAY DIFFRACTIONr_nbd_refined0.2030.2640
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1720.22801
X-RAY DIFFRACTIONr_nbtor_refined0.1570.21561
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.21472
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2120
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0480.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.240.22
X-RAY DIFFRACTIONr_nbd_other0.1880.233
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0410.22
X-RAY DIFFRACTIONr_mcbond_it1.5473.5851638
X-RAY DIFFRACTIONr_mcbond_other1.5473.5831637
X-RAY DIFFRACTIONr_mcangle_it2.4195.3712051
X-RAY DIFFRACTIONr_mcangle_other2.4185.3732052
X-RAY DIFFRACTIONr_scbond_it1.873.9451646
X-RAY DIFFRACTIONr_scbond_other1.8693.9481647
X-RAY DIFFRACTIONr_scangle_it2.9515.8392434
X-RAY DIFFRACTIONr_scangle_other2.955.8422435
X-RAY DIFFRACTIONr_lrange_it4.64343.3543494
X-RAY DIFFRACTIONr_lrange_other4.64343.2923483
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.92-1.970.3251140.3572610X-RAY DIFFRACTION95.9493
1.97-2.0240.3161300.3292612X-RAY DIFFRACTION99.6004
2.024-2.0830.3181430.3042513X-RAY DIFFRACTION99.7746
2.083-2.1470.2791300.272480X-RAY DIFFRACTION100
2.147-2.2170.2591330.2412369X-RAY DIFFRACTION99.96
2.217-2.2950.2421430.232295X-RAY DIFFRACTION100
2.295-2.3820.2461380.2112229X-RAY DIFFRACTION99.9578
2.382-2.4790.2391200.1952169X-RAY DIFFRACTION99.9127
2.479-2.5890.2641000.1982080X-RAY DIFFRACTION99.9542
2.589-2.7150.1971020.1781985X-RAY DIFFRACTION100
2.715-2.8620.217950.1881910X-RAY DIFFRACTION99.8009
2.862-3.0360.223900.1761799X-RAY DIFFRACTION100
3.036-3.2450.193910.1881682X-RAY DIFFRACTION99.9436
3.245-3.5050.17940.1791576X-RAY DIFFRACTION100
3.505-3.8390.188690.1731474X-RAY DIFFRACTION99.9352
3.839-4.2910.199670.1541333X-RAY DIFFRACTION99.6441
4.291-4.9540.173650.1351199X-RAY DIFFRACTION99.842
4.954-6.0640.225670.188995X-RAY DIFFRACTION99.812
6.064-8.5630.201350.176811X-RAY DIFFRACTION99.7642
8.563-66.20.208260.181482X-RAY DIFFRACTION99.2188
Refinement TLS params.Method: refined / Origin x: -8.3427 Å / Origin y: -9.2761 Å / Origin z: 20.2902 Å
111213212223313233
T0.0312 Å20.0131 Å2-0.0097 Å2-0.0154 Å20.0053 Å2--0.0136 Å2
L1.1571 °20.2237 °20.1903 °2-1.9532 °2-0.6285 °2--3.1541 °2
S0.0027 Å °-0.0601 Å °-0.0961 Å °-0.0637 Å °0.065 Å °0.0697 Å °0.0313 Å °-0.0755 Å °-0.0677 Å °
Refinement TLS groupSelection: ALL

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