[English] 日本語
Yorodumi
- PDB-6inf: a glycosyltransferase complex with UDP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6inf
Titlea glycosyltransferase complex with UDP
ComponentsUDP-glycosyltransferase 76G1
KeywordsTRANSFERASE / complex
Function / homology
Function and homology information


steviolbioside glucosyltransferase activity (rebaudioside B forming) / stevioside glucosyltransferase activity (rebaudioside A forming) / quercetin 3-O-glucosyltransferase activity / quercetin 7-O-glucosyltransferase activity / UDP-glucosyltransferase activity / Transferases; Glycosyltransferases; Hexosyltransferases
Similarity search - Function
UDP-glucoronosyl and UDP-glucosyl transferase / UDP-glucuronosyl/UDP-glucosyltransferase / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
URIDINE-5'-DIPHOSPHATE / UDP-glycosyltransferase 76G1
Similarity search - Component
Biological speciesStevia rebaudiana (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsZhu, X. / Yang, T. / Naismith, J.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31771910 China
CitationJournal: Nat Commun / Year: 2019
Title: Hydrophobic recognition allows the glycosyltransferase UGT76G1 to catalyze its substrate in two orientations.
Authors: Yang, T. / Zhang, J. / Ke, D. / Yang, W. / Tang, M. / Jiang, J. / Cheng, G. / Li, J. / Cheng, W. / Wei, Y. / Li, Q. / Naismith, J.H. / Zhu, X.
History
DepositionOct 25, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 31, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: UDP-glycosyltransferase 76G1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5622
Polymers53,1581
Non-polymers4041
Water3,459192
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area710 Å2
ΔGint-8 kcal/mol
Surface area19080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.662, 97.662, 89.626
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-791-

HOH

-
Components

#1: Protein UDP-glycosyltransferase 76G1


Mass: 53158.227 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Stevia rebaudiana (plant) / Gene: UGT76G1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q6VAB4, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: UDP*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 47.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M sodium citrate buffer at pH 5.4 and 20% PEG 4000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.69→49.58 Å / Num. obs: 56938 / % possible obs: 100 % / Redundancy: 19.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.022 / Rrim(I) all: 0.072 / Net I/σ(I): 20.2
Reflection shellResolution: 1.69→1.73 Å / Rmerge(I) obs: 1.007 / Mean I/σ(I) obs: 4 / Num. measured obs: 81062 / Num. unique obs: 4173 / CC1/2: 0.948 / Rpim(I) all: 0.333 / Rrim(I) all: 1.061

-
Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PQ6

2pq6


Resolution: 1.69→48.83 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.954 / SU B: 4.158 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.097 / ESU R Free: 0.095 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20744 2853 5 %RANDOM
Rwork0.1782 ---
obs0.1797 53830 97.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 38.083 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0.01 Å20 Å2
2---0.01 Å20 Å2
3---0.05 Å2
Refinement stepCycle: 1 / Resolution: 1.69→48.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3582 0 25 192 3799
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0193810
X-RAY DIFFRACTIONr_bond_other_d0.0020.023603
X-RAY DIFFRACTIONr_angle_refined_deg1.4891.9685187
X-RAY DIFFRACTIONr_angle_other_deg0.95138317
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5445471
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.83323.898177
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.18915662
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.221526
X-RAY DIFFRACTIONr_chiral_restr0.0880.2565
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214320
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02892
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_it1.6051.8971845
X-RAY DIFFRACTIONr_mcbond_other1.6021.8971844
X-RAY DIFFRACTIONr_mcangle_it2.4922.8342323
X-RAY DIFFRACTIONr_mcangle_other2.4912.8342324
X-RAY DIFFRACTIONr_scbond_it2.0082.1871965
X-RAY DIFFRACTIONr_scbond_other2.0072.1871964
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.23.1932863
X-RAY DIFFRACTIONr_long_range_B_refined5.88116.0544560
X-RAY DIFFRACTIONr_long_range_B_other5.86715.7224473
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.665→1.708 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 156 -
Rwork0.275 2871 -
obs--71.04 %
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)
13.94341.029-0.53361.51080.4511.93120.2974-0.120.44520.0714-0.1280.1034-0.35070.089-0.16940.1608-0.05870.08710.0359-0.01580.110231.5036-6.52717.6325
24.17330.7184-0.69872.97160.0992.29680.1561-0.01370.35730.0704-0.0575-0.0003-0.3031-0.0238-0.09860.1447-0.05320.07080.05860.01250.121438.9667-5.01611.5169
32.42541.3902-0.19811.68190.16920.9136-0.11190.5048-0.2138-0.30050.1471-0.2274-0.05020.0322-0.03520.1928-0.00780.05450.1823-0.01270.152832.7326-23.6702-7.3344
42.029-0.0244-0.67332.0489-0.08612.79260.02230.24350.2253-0.1943-0.03580.26-0.1701-0.44770.01350.06110.02440.01470.15390.02990.13734.0093-19.6506-3.253
53.9754-0.23320.89944.685-1.72432.2605-0.10420.23290.4763-0.17540.1380.7439-0.3325-0.6155-0.03380.19650.13690.00120.29530.02060.32082.6411-12.9041-6.5711
62.45920.34580.03461.5335-0.31041.63530.10050.1474-0.03390.0165-0.0874-0.03840.0819-0.1135-0.01310.079-0.02040.03740.0342-0.00770.030917.9176-27.89320.2872
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 80
2X-RAY DIFFRACTION2A81 - 133
3X-RAY DIFFRACTION3A134 - 261
4X-RAY DIFFRACTION4A262 - 305
5X-RAY DIFFRACTION5A306 - 334
6X-RAY DIFFRACTION6A335 - 459

+
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