[English] 日本語
Yorodumi
- PDB-7yan: UDP-glucuronosyltransferase2B17 C-terminal domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7yan
TitleUDP-glucuronosyltransferase2B17 C-terminal domain
ComponentsUDP-glucuronosyltransferase 2B17
KeywordsTRANSFERASE / Complex / truncation
Function / homology
Function and homology information


: / glucuronosyltransferase / Glucuronidation / glucuronosyltransferase activity / estrogen metabolic process / Prednisone ADME / Aspirin ADME / steroid metabolic process / xenobiotic metabolic process / endoplasmic reticulum membrane / membrane
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
L(+)-TARTARIC ACID / UDP-glucuronosyltransferase 2B17
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsWang, C.Y. / Zhang, L.
Funding support China, 1items
OrganizationGrant numberCountry
Other government China
CitationJournal: To Be Published
Title: UDP-glucuronosyltransferase2B17 C-terminal domain
Authors: Wang, C.Y. / Zhang, L.
History
DepositionJun 28, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: UDP-glucuronosyltransferase 2B17
B: UDP-glucuronosyltransferase 2B17
C: UDP-glucuronosyltransferase 2B17
D: UDP-glucuronosyltransferase 2B17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,7858
Polymers84,1854
Non-polymers6004
Water82946
1
A: UDP-glucuronosyltransferase 2B17
B: UDP-glucuronosyltransferase 2B17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3934
Polymers42,0932
Non-polymers3002
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint-11 kcal/mol
Surface area14390 Å2
MethodPISA
2
C: UDP-glucuronosyltransferase 2B17
hetero molecules

D: UDP-glucuronosyltransferase 2B17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3934
Polymers42,0932
Non-polymers3002
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
Buried area2560 Å2
ΔGint-11 kcal/mol
Surface area14280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.150, 57.308, 74.074
Angle α, β, γ (deg.)99.245, 94.715, 90.118
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
UDP-glucuronosyltransferase 2B17 / UDPGT 2B17 / UGT2B17 / C19-steroid-specific UDP-glucuronosyltransferase / C19-steroid-specific UDPGT


Mass: 21046.270 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UGT2B17 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O75795, glucuronosyltransferase
#2: Chemical
ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H6O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 1.89 Å3/Da / Density % sol: 34.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 20% PEG 6000, 0.2M Na-Tartrate, 0.2M KCl, 2% glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54184 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jun 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 2.5→19.11 Å / Num. obs: 20837 / % possible obs: 97.45 % / Redundancy: 2.7 % / CC1/2: 0.985 / Rmerge(I) obs: 0.0978 / Net I/σ(I): 8.05
Reflection shellResolution: 2.5→2.589 Å / Num. unique obs: 2019 / CC1/2: 0.893

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
CrysalisProdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6IPB

6ipb


Resolution: 2.5→19.11 Å / Cor.coef. Fo:Fc: 0.838 / Cor.coef. Fo:Fc free: 0.763 / SU B: 17.612 / SU ML: 0.388 / Cross valid method: THROUGHOUT / ESU R Free: 0.432
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.3308 1012 4.857 %
Rwork0.2677 19825 -
all0.271 --
obs-20837 97.469 %
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: 18.094 Å2
Baniso -1Baniso -2Baniso -3
1-0.008 Å20.001 Å20.025 Å2
2--0.002 Å2-0.027 Å2
3----0.006 Å2
Refinement stepCycle: LAST / Resolution: 2.5→19.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5052 0 40 46 5138
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0135196
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174907
X-RAY DIFFRACTIONr_angle_refined_deg1.4591.6447014
X-RAY DIFFRACTIONr_angle_other_deg1.1381.57611473
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8585651
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.60724.182220
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.18415941
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8021516
X-RAY DIFFRACTIONr_chiral_restr0.0510.2692
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025688
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02944
X-RAY DIFFRACTIONr_nbd_refined0.2110.21182
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1980.24689
X-RAY DIFFRACTIONr_nbtor_refined0.1560.22432
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.22196
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.2132
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1430.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3040.241
X-RAY DIFFRACTIONr_nbd_other0.3360.2163
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.4140.21
X-RAY DIFFRACTIONr_mcbond_it1.2251.892613
X-RAY DIFFRACTIONr_mcbond_other1.2241.8892612
X-RAY DIFFRACTIONr_mcangle_it2.1532.8313260
X-RAY DIFFRACTIONr_mcangle_other2.1532.8323261
X-RAY DIFFRACTIONr_scbond_it1.1082.0032583
X-RAY DIFFRACTIONr_scbond_other1.1082.0042580
X-RAY DIFFRACTIONr_scangle_it1.9172.9413754
X-RAY DIFFRACTIONr_scangle_other1.9172.9413753
X-RAY DIFFRACTIONr_lrange_it4.68822.4325671
X-RAY DIFFRACTIONr_lrange_other4.68922.4335668
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.5650.448700.3031434X-RAY DIFFRACTION92.8395
2.565-2.6350.423740.2991399X-RAY DIFFRACTION97.2277
2.635-2.7110.424690.2991431X-RAY DIFFRACTION98.7492
2.711-2.7950.388770.291336X-RAY DIFFRACTION99.3671
2.795-2.8860.327860.3251346X-RAY DIFFRACTION99.5828
2.886-2.9870.445670.3081302X-RAY DIFFRACTION99.7087
2.987-3.10.325640.2811210X-RAY DIFFRACTION99.376
3.1-3.2260.352490.271212X-RAY DIFFRACTION99.6051
3.226-3.3690.324490.2441165X-RAY DIFFRACTION99.0212
3.369-3.5330.314400.2571107X-RAY DIFFRACTION99.3934
3.533-3.7240.347500.2581030X-RAY DIFFRACTION98.7203
3.724-3.9490.264440.245979X-RAY DIFFRACTION97.6145
3.949-4.2210.245500.227916X-RAY DIFFRACTION98.0711
4.221-4.5580.271410.235842X-RAY DIFFRACTION97.033
4.558-4.9910.326440.256766X-RAY DIFFRACTION96.5435
4.991-5.5770.293470.271696X-RAY DIFFRACTION96.8709
5.577-6.4340.352300.273616X-RAY DIFFRACTION96.4179
6.434-7.8640.277330.256497X-RAY DIFFRACTION93.8053
7.864-11.0570.216200.223379X-RAY DIFFRACTION91.3044
11.057-19.110.23380.286162X-RAY DIFFRACTION68.5484

+
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