[English] 日本語
Yorodumi
- PDB-7erx: Glycosyltransferase in complex with UDP and STB -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7erx
TitleGlycosyltransferase in complex with UDP and STB
ComponentsGlycosyltransferase
KeywordsTRANSFERASE / glycosyltransferase in steviol glucosylation
Function / homologyUDP-glucosyltransferase activity / UDP-glycosyltransferase family, conserved site / UDP-glycosyltransferases signature. / UDP-glucoronosyl and UDP-glucosyl transferase / UDP-glucuronosyl/UDP-glucosyltransferase / Transferases; Glycosyltransferases; Hexosyltransferases / Steviolbioside / URIDINE-5'-DIPHOSPHATE / Glycosyltransferase
Function and homology information
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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 / Glycerol


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


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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more