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- PDB-7ery: apo form of the glycosyltransferase -

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Basic information

Entry
Database: PDB / ID: 7ery
Titleapo form of the glycosyltransferase
ComponentsGlycosyltransferase
KeywordsTRANSFERASE / glycosyltransferase apo form
Function / homology: / UDP-glucosyltransferase activity / UDP-glycosyltransferase family, conserved site / UDP-glycosyltransferases signature. / UDP-glucoronosyl and UDP-glucosyl transferase / UDP-glucuronosyl/UDP-glucosyltransferase / Transferases; Glycosyltransferases; Hexosyltransferases / nucleotide binding / Glycosyltransferase
Function and homology information
Biological speciesOryza sativa subsp. japonica (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 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 1.2Apr 3, 2024Group: 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

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Assembly

Deposited unit
A: Glycosyltransferase


Theoretical massNumber of molelcules
Total (without water)51,0421
Polymers51,0421
Non-polymers00
Water3,441191
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area17060 Å2
Unit cell
Length a, b, c (Å)50.268, 79.837, 105.413
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / 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: 2.12 Å3/Da / Density % sol: 41.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 4000 HEPES-NaOH buffer pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.77→50 Å / Num. obs: 42109 / % possible obs: 99.9 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 35
Reflection shellResolution: 1.77→1.8 Å / Rmerge(I) obs: 0.284 / Num. unique obs: 2074

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: partial model from a low resolution SAD data

Resolution: 1.77→39.95 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.951 / SU B: 4.219 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.103
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1977 2006 4.764 %
Rwork0.1658 40099 -
all0.167 --
obs-42105 99.898 %
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 30.859 Å2
Baniso -1Baniso -2Baniso -3
1-0.795 Å2-0 Å2-0 Å2
2--0.054 Å2-0 Å2
3----0.849 Å2
Refinement stepCycle: LAST / Resolution: 1.77→39.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3114 0 0 191 3305
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0133220
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173095
X-RAY DIFFRACTIONr_angle_refined_deg1.5491.6324381
X-RAY DIFFRACTIONr_angle_other_deg1.4061.5717110
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1125412
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.00219.94166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.93615513
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1141531
X-RAY DIFFRACTIONr_chiral_restr0.0790.2408
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023650
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02744
X-RAY DIFFRACTIONr_nbd_refined0.2050.2668
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1710.22944
X-RAY DIFFRACTIONr_nbtor_refined0.1620.21584
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.21570
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1240.2163
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1940.211
X-RAY DIFFRACTIONr_nbd_other0.1940.248
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1810.28
X-RAY DIFFRACTIONr_mcbond_it2.1782.0321645
X-RAY DIFFRACTIONr_mcbond_other2.1772.031644
X-RAY DIFFRACTIONr_mcangle_it3.0713.0382058
X-RAY DIFFRACTIONr_mcangle_other3.0713.042059
X-RAY DIFFRACTIONr_scbond_it3.4522.4351575
X-RAY DIFFRACTIONr_scbond_other3.4512.4361576
X-RAY DIFFRACTIONr_scangle_it4.9913.4992323
X-RAY DIFFRACTIONr_scangle_other4.9913.52324
X-RAY DIFFRACTIONr_lrange_it6.51725.3993571
X-RAY DIFFRACTIONr_lrange_other6.48525.0783537
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.77-1.8160.2191460.1862929X-RAY DIFFRACTION99.5468
1.816-1.8660.2531440.1712843X-RAY DIFFRACTION100
1.866-1.920.2011350.1662762X-RAY DIFFRACTION100
1.92-1.9790.191340.1642683X-RAY DIFFRACTION100
1.979-2.0440.1961310.1592615X-RAY DIFFRACTION100
2.044-2.1150.1981290.1622535X-RAY DIFFRACTION100
2.115-2.1950.2041200.1572449X-RAY DIFFRACTION100
2.195-2.2840.2031210.1552376X-RAY DIFFRACTION100
2.284-2.3860.2071120.1642259X-RAY DIFFRACTION100
2.386-2.5020.2081080.1572167X-RAY DIFFRACTION100
2.502-2.6370.2051030.1612078X-RAY DIFFRACTION100
2.637-2.7970.178990.1741955X-RAY DIFFRACTION100
2.797-2.990.186920.1661857X-RAY DIFFRACTION100
2.99-3.2290.2870.1841727X-RAY DIFFRACTION100
3.229-3.5360.181800.1811595X-RAY DIFFRACTION100
3.536-3.9520.196740.1611455X-RAY DIFFRACTION100
3.952-4.560.196640.151305X-RAY DIFFRACTION99.927
4.56-5.5780.184560.1651121X-RAY DIFFRACTION100
5.578-7.8580.21440.185874X-RAY DIFFRACTION100
7.858-39.950.214270.159514X-RAY DIFFRACTION96.6071
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)
11.45940.5271-0.1061.4045-0.06790.72130.0464-0.0245-0.1968-0.0658-0.0405-0.16760.05030.1098-0.00580.0228-0.0031-0.00770.03530.00220.066815.72122.51321.197
20.9549-0.1647-0.06460.6947-0.11861.58760.04110.05420.1186-0.11950.0160.09260.0009-0.0498-0.0570.0241-0.0063-0.00680.0360.01450.0571.81935.32420.457
31.10820.61180.37851.14910.10532.2710.1384-0.107-0.03470.25230.0121-0.07650.15530.0063-0.15060.19870.0005-0.04810.0982-0.01030.054910.4329.89550.164
42.46190.55161.05640.66720.70263.34520.1892-0.0744-0.08890.1070.0207-0.11490.13410.2321-0.20990.24760.0151-0.07620.1399-0.02770.124520.13232.40554.17
51.06360.3631.36490.66340.35342.9288-0.0092-0.10040.09730.24640.00090.0592-0.2384-0.17190.00830.15190.0190.00810.0743-0.01790.06783.7838.15142.901
62.1285-0.1668-0.2832.00062.57786.39280.0076-0.0034-0.19090.0691-0.07350.21690.1439-0.44470.06590.0146-0.0246-0.01090.07460.02420.0849-7.32525.00826.239
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA13 - 144
2X-RAY DIFFRACTION2ALLA145 - 251
3X-RAY DIFFRACTION3ALLA252 - 312
4X-RAY DIFFRACTION4ALLA313 - 338
5X-RAY DIFFRACTION5ALLA339 - 433
6X-RAY DIFFRACTION6ALLA434 - 460

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