[English] 日本語
Yorodumi
- PDB-8dhw: Treponema lecithinolyticum beta-glucuronidase in complex with a U... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8dhw
TitleTreponema lecithinolyticum beta-glucuronidase in complex with a UNC4917-glucuronide conjugate
ComponentsGlycosyl hydrolase family 2, TIM barrel domain protein
KeywordsHYDROLASE / Glycoside hydrolase family 2 / TIM barrel domain
Function / homologyGlycosidases / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / Chem-E0V / :
Function and homology information
Biological speciesTreponema lecithinolyticum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsLietzan, A.D. / Redinbo, M.R.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM137286 United States
National Institutes of Health/National Center for Advancing Translational Sciences (NIH/NCATS)TR002489 United States
CitationJournal: Sci Adv / Year: 2023
Title: Microbial beta-glucuronidases drive human periodontal disease etiology.
Authors: Lietzan, A.D. / Simpson, J.B. / Walton, W.G. / Jariwala, P.B. / Xu, Y. / Boynton, M.H. / Liu, J. / Redinbo, M.R.
History
DepositionJun 28, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 17, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 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: Glycosyl hydrolase family 2, TIM barrel domain protein
B: Glycosyl hydrolase family 2, TIM barrel domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,53515
Polymers144,4672
Non-polymers2,06813
Water16,538918
1
A: Glycosyl hydrolase family 2, TIM barrel domain protein
B: Glycosyl hydrolase family 2, TIM barrel domain protein
hetero molecules

A: Glycosyl hydrolase family 2, TIM barrel domain protein
B: Glycosyl hydrolase family 2, TIM barrel domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)293,06930
Polymers288,9344
Non-polymers4,13626
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area21500 Å2
ΔGint-374 kcal/mol
Surface area73350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.485, 94.485, 287.607
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein Glycosyl hydrolase family 2, TIM barrel domain protein / Beta-glucuronidase


Mass: 72233.453 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Treponema lecithinolyticum (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: U2KI81, beta-glucuronidase
#2: Chemical ChemComp-E0V / 4-(4-beta-D-glucopyranuronosylpiperazin-1-yl)-2,7-bis(methylamino)pyrido[3',2':4,5]thieno[3,2-d]pyrimidine


Mass: 505.547 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O6S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 918 / 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: 2.26 Å3/Da / Density % sol: 45.7 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 2.4 M ammonium sulfate, 0.1 M MOPS

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03319 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 2, 2021
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03319 Å / Relative weight: 1
ReflectionResolution: 1.75→49.13 Å / Num. obs: 131523 / % possible obs: 99.7 % / Redundancy: 10 % / Biso Wilson estimate: 27.12 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.028 / Rrim(I) all: 0.092 / Net I/σ(I): 14.4 / Num. measured all: 1317703 / Scaling rejects: 31
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.75-1.784.11.2912478560960.4650.71.478195.3
9.59-49.139.50.04592509750.9990.0150.04841.799.5

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.7data scaling
PHASERphasing
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BJQ

6bjq


Resolution: 1.75→49.13 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 21.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2115 1995 1.52 %
Rwork0.1732 129165 -
obs0.1738 131160 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 76.16 Å2 / Biso mean: 30.8596 Å2 / Biso min: 17.89 Å2
Refinement stepCycle: final / Resolution: 1.75→49.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9351 0 125 918 10394
Biso mean--42.29 37.63 -
Num. residues----1179
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.75-1.790.3081340.28138668880295
1.79-1.840.27171400.25399088922899
1.84-1.90.23511420.232291389280100
1.9-1.960.34741410.256191369277100
1.96-2.030.25221420.187391749316100
2.03-2.110.23511410.173191689309100
2.11-2.20.22731430.172392079350100
2.2-2.320.21791390.19449068920798
2.32-2.470.21791430.17292279370100
2.47-2.660.20821420.176992549396100
2.66-2.920.21921430.182793039446100
2.92-3.350.19991460.171493819527100
3.35-4.220.18621450.14494569601100
4.22-49.130.18951540.1569989710051100

+
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