[English] 日本語
Yorodumi
- PDB-5uxf: Crystal Structure of mouse RECON (AKR1C13) in complex with Cyclic... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5uxf
TitleCrystal Structure of mouse RECON (AKR1C13) in complex with Cyclic di-AMP
ComponentsDihydrodiol dehydrogenase
KeywordsOXIDOREDUCTASE / Cyclic di-AMP / Aldo-keto reductase / TIM barrel
Function / homology
Function and homology information


: / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / xenobiotic metabolic process / oxidoreductase activity
Similarity search - Function
Aldo-keto reductase family 1 member C / Aldo/keto reductase family signature 1. / NADP-dependent oxidoreductase domain / Aldo/keto reductase family signature 2. / Aldo/keto reductase, conserved site / Aldo-keto reductase / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily / TIM Barrel ...Aldo-keto reductase family 1 member C / Aldo/keto reductase family signature 1. / NADP-dependent oxidoreductase domain / Aldo/keto reductase family signature 2. / Aldo/keto reductase, conserved site / Aldo-keto reductase / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-2BA / Dihydrodiol dehydrogenase / Aldo-keto reductase family 1 member C13
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.501 Å
AuthorsLuo, S. / Tong, L.
CitationJournal: Immunity / Year: 2017
Title: Sensing of Bacterial Cyclic Dinucleotides by the Oxidoreductase RECON Promotes NF-kappa B Activation and Shapes a Proinflammatory Antibacterial State.
Authors: McFarland, A.P. / Luo, S. / Ahmed-Qadri, F. / Zuck, M. / Thayer, E.F. / Goo, Y.A. / Hybiske, K. / Tong, L. / Woodward, J.J.
History
DepositionFeb 22, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Mar 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Dihydrodiol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9492
Polymers39,2911
Non-polymers6581
Water7,782432
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.644, 75.422, 88.416
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Dihydrodiol dehydrogenase


Mass: 39291.031 Da / Num. of mol.: 1 / Fragment: RECON / Mutation: K68A, K70A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Akr1c13, ddh / Plasmid: pSpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q54A37, UniProt: Q8VC28*PLUS
#2: Chemical ChemComp-2BA / (2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-2,9-bis(6-amino-9H-purin-9-yl)octahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8 ]tetraoxadiphosphacyclododecine-3,5,10,12-tetrol 5,12-dioxide / bis-(3',5')-cyclic-dimeric-Adenosine-monophosphate


Mass: 658.412 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H24N10O12P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 432 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.05 Å3/Da / Density % sol: 39.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.2 M NaCl, 0.1 M Bis-Tris, pH5.5, 25% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 21, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.5→25 Å / Num. obs: 52009 / % possible obs: 98.9 % / Redundancy: 5.7 % / Biso Wilson estimate: 13.06 Å2 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.034 / Rrim(I) all: 0.085 / Χ2: 1.043 / Net I/σ(I): 18.1 / Num. measured all: 295963
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.5-1.5530.2420.9250.1590.2911.0992.7
1.55-1.623.90.2070.950.1180.2391.07399.1
1.62-1.695.70.1820.9760.0820.21.051100
1.69-1.786.40.1480.9860.0630.1611.012100
1.78-1.896.40.1240.990.0530.1351.032100
1.89-2.046.40.1020.9910.0440.1111.032100
2.04-2.246.40.0880.9930.0370.0951.041100
2.24-2.566.40.0790.9940.0340.0860.998100
2.56-3.236.30.0760.9940.0330.0831.082100
3.23-255.70.0580.9950.0260.0641.06897.2

-
Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
PDB_EXTRACT3.22data extraction
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.501→24.182 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.13
RfactorNum. reflection% reflection
Rfree0.1861 2623 5.05 %
Rwork0.1679 --
obs0.1688 51925 98.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 51.31 Å2 / Biso mean: 17.2153 Å2 / Biso min: 6.68 Å2
Refinement stepCycle: final / Resolution: 1.501→24.182 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2526 0 44 432 3002
Biso mean--14.23 26.78 -
Num. residues----316
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062631
X-RAY DIFFRACTIONf_angle_d0.9773570
X-RAY DIFFRACTIONf_chiral_restr0.057393
X-RAY DIFFRACTIONf_plane_restr0.006454
X-RAY DIFFRACTIONf_dihedral_angle_d14.7911600
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5014-1.52860.20421170.1812203232085
1.5286-1.5580.19451320.17222459259196
1.558-1.58980.19851340.16272537267198
1.5898-1.62440.2111400.164226162756100
1.6244-1.66220.17451380.157826002738100
1.6622-1.70370.18461380.159326022740100
1.7037-1.74980.15351390.16126112750100
1.7498-1.80130.18691400.165626332773100
1.8013-1.85940.20441370.169725742711100
1.8594-1.92580.1991400.185526232763100
1.9258-2.00290.2261390.171626142753100
2.0029-2.0940.21451400.168126282768100
2.094-2.20430.18951390.163426132752100
2.2043-2.34230.18051370.17926252762100
2.3423-2.5230.18851420.174926602802100
2.523-2.77660.21091400.178326372777100
2.7766-3.17760.21541430.182126772820100
3.1776-4.00050.15751400.15432620276097
4.0005-24.18520.15321480.1562770291898

+
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