[English] 日本語
Yorodumi
- PDB-6t88: Urocanate reductase in complex with imidazole propionate -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6t88
TitleUrocanate reductase in complex with imidazole propionate
ComponentsUrocanate reductase
KeywordsOXIDOREDUCTASE / urocanate reductase / bacterial enzyme
Function / homology
Function and homology information


urocanate reductase / FMN binding / oxidoreductase activity / plasma membrane
Similarity search - Function
Flavocytochrome c / FMN-binding / FMN-binding domain / FMN_bind / Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain superfamily / FAD-dependent oxidoreductase 2, FAD binding domain / FAD binding domain / FAD/NAD(P)-binding domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / 3-(1~{H}-imidazol-5-yl)propanoic acid / Urocanate reductase
Similarity search - Component
Biological speciesShewanella oneidensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsVenskutonyte, R. / Lindkvist-Petersson, K.
Funding support Sweden, 3items
OrganizationGrant numberCountry
Swedish Research Council2016-01319 Sweden
Swedish Research Council2017-05816 Sweden
European Research Council780659 Sweden
CitationJournal: Nat Commun / Year: 2021
Title: Structural characterization of the microbial enzyme urocanate reductase mediating imidazole propionate production.
Authors: Venskutonyte, R. / Koh, A. / Stenstrom, O. / Khan, M.T. / Lundqvist, A. / Akke, M. / Backhed, F. / Lindkvist-Petersson, K.
History
DepositionOct 24, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 10, 2021Group: 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 1.2Jan 24, 2024Group: 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: Urocanate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,77615
Polymers49,9851
Non-polymers1,79214
Water11,458636
1
A: Urocanate reductase
hetero molecules

A: Urocanate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,55330
Polymers99,9692
Non-polymers3,58428
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area9780 Å2
ΔGint-123 kcal/mol
Surface area31910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.834, 123.834, 66.294
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-1263-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Urocanate reductase


Mass: 49984.523 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Truncated UrdA, construct comprising residues 130-582 and a C-terminal 6xHis tag.
Source: (gene. exp.) Shewanella oneidensis (strain MR-1) (bacteria)
Strain: MR-1 / Gene: urdA, SO_4620 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8CVD0, urocanate reductase

-
Non-polymers , 6 types, 650 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical ChemComp-MWQ / 3-(1~{H}-imidazol-5-yl)propanoic acid


Mass: 140.140 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8N2O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 636 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.94 Å3/Da / Density % sol: 58.1 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 20 % PEG8000 0.2 M NH4Cl 0.1 M HEPES pH 7.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→45.25 Å / Num. obs: 114880 / % possible obs: 100 % / Redundancy: 21.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.025 / Rrim(I) all: 0.119 / Net I/σ(I): 17.7 / Num. measured all: 2433789 / Scaling rejects: 183
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
1.4-1.4221.81.65712375956760.7820.361.6962.5100
7.67-45.2520.80.051162097810.9990.0110.05252.499.6

-
Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
PHENIX1.14-3260refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1D4C

1d4c


Resolution: 1.4→45.25 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 14.06
RfactorNum. reflection% reflection
Rfree0.1461 5725 4.99 %
Rwork0.1156 --
obs0.1172 114835 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 73.34 Å2 / Biso mean: 20.5588 Å2 / Biso min: 8.36 Å2
Refinement stepCycle: final / Resolution: 1.4→45.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3455 0 260 644 4359
Biso mean--28.01 34.51 -
Num. residues----454

+
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