[English] 日本語
Yorodumi
- PDB-7qe2: Crystal structure of D-glucuronic acid bound to SN243 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7qe2
TitleCrystal structure of D-glucuronic acid bound to SN243
ComponentsSN243
KeywordsHYDROLASE / enzyme discovery / carbohydrate-active enzymes (CAZy) / protein engineering / functional metagenomics)
Function / homologyACETATE ION / beta-D-glucopyranuronic acid
Function and homology information
Biological speciesunidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsNeun, S. / Brear, P. / Campbell, E. / Omari, K. / Wagner, O. / Hyvonen, M. / Hollfelder, F.
Funding support1items
OrganizationGrant numberCountry
European Union (EU)Metafluidics, 685474
CitationJournal: Nat.Chem.Biol. / Year: 2022
Title: Functional metagenomic screening identifies an unexpected beta-glucuronidase.
Authors: Neun, S. / Brear, P. / Campbell, E. / Tryfona, T. / El Omari, K. / Wagner, A. / Dupree, P. / Hyvonen, M. / Hollfelder, F.
History
DepositionDec 1, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 12, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2023Group: 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 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SN243
B: SN243
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,82442
Polymers163,8342
Non-polymers2,99040
Water6,648369
1
A: SN243
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,70125
Polymers81,9171
Non-polymers1,78424
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SN243
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,12317
Polymers81,9171
Non-polymers1,20616
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.230, 82.180, 93.180
Angle α, β, γ (deg.)66.740, 89.260, 89.340
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 40 through 354 or resid 356 through 623 or resid 625 through 831))
21(chain B and (resid 40 through 202 or resid 204...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 40 through 354 or resid 356 through 623 or resid 625 through 831))A40 - 354
121(chain A and (resid 40 through 354 or resid 356 through 623 or resid 625 through 831))A356 - 623
131(chain A and (resid 40 through 354 or resid 356 through 623 or resid 625 through 831))A625 - 831
211(chain B and (resid 40 through 202 or resid 204...B40 - 202
221(chain B and (resid 40 through 202 or resid 204...B204 - 354
231(chain B and (resid 40 through 202 or resid 204...B356 - 623
241(chain B and (resid 40 through 202 or resid 204...B625 - 785
251(chain B and (resid 40 through 202 or resid 204...B831

-
Components

-
Protein / Sugars , 2 types, 4 molecules AB

#1: Protein SN243


Mass: 81916.852 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified (others) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Sugar ChemComp-BDP / beta-D-glucopyranuronic acid / beta-D-glucuronic acid / D-glucuronic acid / glucuronic acid


Type: D-saccharide, beta linking / Mass: 194.139 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H10O7 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpAbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranuronic acidCOMMON NAMEGMML 1.0
b-D-GlcpAIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcASNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 4 types, 407 molecules

#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical...
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 33 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 369 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.69 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M MES pH 6.5, 0.01 M ZnSO4 and 25% PEG MME 550

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Apr 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.15→48.31 Å / Num. obs: 91233 / % possible obs: 97.3 % / Redundancy: 3.6 % / CC1/2: 0.995 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.067 / Rrim(I) all: 0.126 / Net I/σ(I): 7.1 / Num. measured all: 325221
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.7 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.15-2.211.652502567400.3530.9961.930.997.3
9.62-48.310.03935809570.9980.0230.04523.291.1

-
Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7QE1

7qe1


Resolution: 2.15→48.306 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 29.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2395 4763 5.22 %
Rwork0.196 86435 -
obs0.1982 91198 97.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 133.75 Å2 / Biso mean: 57.726 Å2 / Biso min: 34.68 Å2
Refinement stepCycle: final / Resolution: 2.15→48.306 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11229 0 83 370 11682
Biso mean--79.67 58.14 -
Num. residues----1476
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4454X-RAY DIFFRACTION6.466TORSIONAL
12B4454X-RAY DIFFRACTION6.466TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.15-2.17450.43521660.374290297
2.1745-2.20.41431790.3606280697
2.2-2.22690.33591900.3364288697
2.2269-2.25510.35121830.3336285597
2.2551-2.28470.36651550.3141289398
2.2847-2.3160.30011370.2995289998
2.316-2.34910.34381760.2891287197
2.3491-2.38420.311620.2785284398
2.3842-2.42140.32241500.2734295798
2.4214-2.46110.29791800.2578285498
2.4611-2.50360.31671610.2499290798
2.5036-2.54910.31911870.2427288498
2.5491-2.59810.26231410.2305291998
2.5981-2.65110.25531440.2228294898
2.6511-2.70880.28671240.2198288698
2.7088-2.77180.30861260.2163296198
2.7718-2.84110.27641760.2175289898
2.8411-2.91790.27021780.2063287298
2.9179-3.00370.24751450.2021296598
3.0037-3.10070.25151680.1907286998
3.1007-3.21150.23161640.1834292398
3.2115-3.340.21341500.185292798
3.34-3.4920.23871630.1825288698
3.492-3.67610.2351990.1804280497
3.6761-3.90630.19731510.169287096
3.9063-4.20770.19621310.1595283695
4.2077-4.63090.22911470.1567281895
4.6309-5.30020.18841240.1657285696
5.3002-6.67490.22111440.1986285196
6.6749-48.3060.1971620.1761278994

+
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