[English] 日本語
Yorodumi
- PDB-5gl5: Sterol 3-beta-glucosyltransferase (ugt51) from Saccharomyces cere... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5gl5
TitleSterol 3-beta-glucosyltransferase (ugt51) from Saccharomyces cerevisiae (strain ATCC 204508 / S288c): UDPG complex
ComponentsSterol 3-beta-glucosyltransferase
KeywordsTRANSFERASE / glycotransferase / complex / native
Function / homology
Function and homology information


sterol 3beta-glucosyltransferase / sterol 3-beta-glucosyltransferase activity / soladodine glucosyltransferase activity / brassicasterol glucosyltransferase activity / cholesterol alpha-glucosyltransferase activity / ascospore-type prospore membrane formation / sterol biosynthetic process / UDP-glycosyltransferase activity / sterol metabolic process / lipid glycosylation ...sterol 3beta-glucosyltransferase / sterol 3-beta-glucosyltransferase activity / soladodine glucosyltransferase activity / brassicasterol glucosyltransferase activity / cholesterol alpha-glucosyltransferase activity / ascospore-type prospore membrane formation / sterol biosynthetic process / UDP-glycosyltransferase activity / sterol metabolic process / lipid glycosylation / carbohydrate metabolic process / membrane / cytoplasm
Similarity search - Function
Glycosyltransferase family 28, N-terminal domain / Glycosyltransferase family 28 N-terminal domain / domain in glucosyltransferases, myotubularins and other putative membrane-associated proteins / GRAM domain / GRAM domain / UDP-glucoronosyl and UDP-glucosyl transferase / UDP-glucuronosyl/UDP-glucosyltransferase / PH domain / PH domain profile. / Pleckstrin homology domain. ...Glycosyltransferase family 28, N-terminal domain / Glycosyltransferase family 28 N-terminal domain / domain in glucosyltransferases, myotubularins and other putative membrane-associated proteins / GRAM domain / GRAM domain / UDP-glucoronosyl and UDP-glucosyl transferase / UDP-glucuronosyl/UDP-glucosyltransferase / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily
Similarity search - Domain/homology
URIDINE-5'-DIPHOSPHATE-GLUCOSE / Sterol 3-beta-glucosyltransferase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288c (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsFeng, Y. / Chen, L.-Q.
CitationJournal: J. Struct. Biol. / Year: 2018
Title: Structural Dissection of Sterol Glycosyltransferase UGT51 from Saccharomyces cerevisiae for Substrate Specificity.
Authors: Chen, L.-Q. / Zhang, Y. / Feng, Y.
History
DepositionJul 8, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 8, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Sterol 3-beta-glucosyltransferase
B: Sterol 3-beta-glucosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,1354
Polymers112,0022
Non-polymers1,1332
Water5,152286
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4770 Å2
ΔGint-19 kcal/mol
Surface area36260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.660, 80.562, 154.587
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: 0 / Auth seq-ID: 739 - 1170 / Label seq-ID: 39 - 470

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

-
Components

#1: Protein Sterol 3-beta-glucosyltransferase / Autophagy-related protein 26 / UDP-glycosyltransferase 51


Mass: 56001.094 Da / Num. of mol.: 2 / Fragment: UNP residues 722-1198
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / Gene: ATG26, UGT51, YLR189C / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q06321, sterol 3beta-glucosyltransferase
#2: Chemical ChemComp-UPG / URIDINE-5'-DIPHOSPHATE-GLUCOSE / URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER / Uridine diphosphate glucose


Mass: 566.302 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H24N2O17P2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 286 / 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: 1.94 Å3/Da / Density % sol: 36.48 %
Crystal growTemperature: 287.15 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, magnesium chloride, Tris pH8.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9202 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9202 Å / Relative weight: 1
ReflectionResolution: 1.903→77.38 Å / Num. obs: 65564 / % possible obs: 99.9 % / Redundancy: 14.5 % / Rmerge(I) obs: 0.164 / Rsym value: 0.102 / Net I/σ(I): 18.04
Reflection shellResolution: 1.903→1.97 Å / CC1/2: 0.849

-
Processing

Software
NameVersionClassification
REFMAC5.8.0157refinement
HKL-2000data reduction
HKL-2000data scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1rrv
Resolution: 1.9→77.29 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.928 / SU B: 7.427 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R: 0.182 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21936 3095 5 %RANDOM
Rwork0.18535 ---
obs0.18712 58702 89.5 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.331 Å2
Baniso -1Baniso -2Baniso -3
1-0.72 Å20 Å20 Å2
2---0.3 Å20 Å2
3----0.42 Å2
Refinement stepCycle: 1 / Resolution: 1.9→77.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6834 0 72 286 7192
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0197071
X-RAY DIFFRACTIONr_bond_other_d0.0020.026647
X-RAY DIFFRACTIONr_angle_refined_deg1.6791.9639581
X-RAY DIFFRACTIONr_angle_other_deg1.006315410
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4165858
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.62223.811307
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.198151221
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6141540
X-RAY DIFFRACTIONr_chiral_restr0.10.21063
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0217721
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021475
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_it3.6461.4573444
X-RAY DIFFRACTIONr_mcbond_other3.6461.4563443
X-RAY DIFFRACTIONr_mcangle_it4.9282.1624298
X-RAY DIFFRACTIONr_mcangle_other4.9282.1634299
X-RAY DIFFRACTIONr_scbond_it5.7422.0033627
X-RAY DIFFRACTIONr_scbond_other5.7422.0033626
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.0282.7435284
X-RAY DIFFRACTIONr_long_range_B_refined9.3317.5917894
X-RAY DIFFRACTIONr_long_range_B_other9.33617.4717850
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 27226 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.903→1.952 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 81 -
Rwork0.195 1487 -
obs--31.12 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.7435-0.1744-0.30511.2634-0.04781.28720.0023-0.1540.06630.12950.0264-0.2428-0.07420.261-0.02870.0353-0.0238-0.00010.0864-0.02590.07916.849-0.732-40.692
20.9065-0.17760.48810.8328-0.0050.98320.10240.0152-0.19490.0695-0.02620.08730.1963-0.0138-0.07620.058-0.0186-0.00720.0221-0.0120.06133.2370.774-5.47
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A737 - 1171
2X-RAY DIFFRACTION2B739 - 1173

+
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