[English] 日本語
Yorodumi
- PDB-6uts: Crystal Structure of bacterial pirin YhhW in complex with nickel(... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6uts
TitleCrystal Structure of bacterial pirin YhhW in complex with nickel(II) from Escherichia coli
ComponentsQuercetin 2,3-dioxygenase
KeywordsMETAL BINDING PROTEIN / bacterial pirin / nickel binding / quercetinase / OXIDOREDUCTASE
Function / homology
Function and homology information


quercetin 2,3-dioxygenase / quercetin 2,3-dioxygenase activity / dioxygenase activity / metal ion binding
Similarity search - Function
Quercetin 2,3-dioxygenase, C-terminal cupin domain / Quercetinase C-terminal cupin domain / Pirin, N-terminal domain / Pirin / Pirin / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
NICKEL (II) ION / Quercetin 2,3-dioxygenase / Quercetin 2,3-dioxygenase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.09 Å
AuthorsGuo, B. / Zhang, Y. / Jia, Z.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)38855 Canada
CitationJournal: Acs Chem.Biol. / Year: 2019
Title: Structure-Dependent Modulation of Substrate Binding and Biodegradation Activity of Pirin Proteins toward Plant Flavonols.
Authors: Guo, B. / Zhang, Y. / Hicks, G. / Huang, X. / Li, R. / Roy, N. / Jia, Z.
History
DepositionOct 29, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2019Group: Database references / Category: citation / citation_author
Revision 1.2Nov 20, 2019Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / struct_conn
Revision 1.3Jan 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 11, 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: Quercetin 2,3-dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3692
Polymers26,3101
Non-polymers591
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)108.870, 108.870, 83.368
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

-
Components

#1: Protein Quercetin 2,3-dioxygenase


Mass: 26310.367 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12
Gene: FAM12_08410, FAM13_08105, FAZ80_08430, FAZ81_08230, FAZ83_10840, FAZ86_07885, FAZ87_06805
Production host: Escherichia coli (E. coli) / References: UniProt: A0A4S5WTB9, UniProt: P46852*PLUS
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.69 Å3/Da / Density % sol: 73.8 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / pH: 6.5 / Details: 0.1 M MES (pH 6.5) and 14% (w/v) PEG 20,000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03319 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03319 Å / Relative weight: 1
ReflectionResolution: 3.088→28.39 Å / Num. obs: 9553 / % possible obs: 98.9 % / Redundancy: 25 % / CC1/2: 0.99 / Rmerge(I) obs: 0.2 / Rrim(I) all: 0.207 / Net I/σ(I): 15.08
Reflection shellResolution: 3.088→3.102 Å / Num. unique obs: 9607 / CC1/2: 0.678

-
Processing

Software
NameVersionClassification
Blu-Icedata collection
PHENIX1.17.1_3660refinement
XDSdata scaling
PHENIXmodel building
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TQ5

1tq5


Resolution: 3.09→28.39 Å / SU ML: 0.4886 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.1549
RfactorNum. reflection% reflection
Rfree0.2654 955 10 %
Rwork0.2297 --
obs0.2334 9553 99.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 104.23 Å2
Refinement stepCycle: LAST / Resolution: 3.09→28.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1751 0 1 0 1752
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00911795
X-RAY DIFFRACTIONf_angle_d1.09932444
X-RAY DIFFRACTIONf_chiral_restr0.065268
X-RAY DIFFRACTIONf_plane_restr0.0071317
X-RAY DIFFRACTIONf_dihedral_angle_d13.4778241
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.09-3.250.41971300.36831177X-RAY DIFFRACTION97.68
3.25-3.450.28721330.27981192X-RAY DIFFRACTION99.25
3.45-3.720.30751350.2571207X-RAY DIFFRACTION98.89
3.72-4.090.28241330.23011216X-RAY DIFFRACTION99.26
4.09-4.680.2151370.17731225X-RAY DIFFRACTION99.27
4.69-5.890.24171390.21891244X-RAY DIFFRACTION99.71
5.89-28.390.27481480.23721337X-RAY DIFFRACTION99.8

+
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://pdbjlvh1.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