[English] 日本語
Yorodumi
- PDB-5i93: Structure of Mouse Acireductone dioxygenase with Ni2+ and 2-ketop... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5i93
TitleStructure of Mouse Acireductone dioxygenase with Ni2+ and 2-ketopentanoic acid in the active site
Components1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase
KeywordsOXIDOREDUCTASE / 2-oxovaleric acid
Function / homology
Function and homology information


Methionine salvage pathway / acireductone dioxygenase (Ni2+-requiring) / acireductone dioxygenase [iron(II)-requiring] / acireductone dioxygenase (Ni2+-requiring) activity / acireductone dioxygenase [iron(II)-requiring] activity / L-methionine salvage from methylthioadenosine / nickel cation binding / oxidoreductase activity / iron ion binding / nucleus ...Methionine salvage pathway / acireductone dioxygenase (Ni2+-requiring) / acireductone dioxygenase [iron(II)-requiring] / acireductone dioxygenase (Ni2+-requiring) activity / acireductone dioxygenase [iron(II)-requiring] activity / L-methionine salvage from methylthioadenosine / nickel cation binding / oxidoreductase activity / iron ion binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Acireductone dioxygenase, eukaryotes / Acireductone dioxygenase ARD family / ARD/ARD' family / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
2-oxopentanoic acid / NICKEL (II) ION / Acireductone dioxygenase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.236 Å
AuthorsDeshpande, A.R. / Wagenpfeil, K. / Pochapsky, T.C. / Petsko, G.A. / Ringe, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM26788 United States
CitationJournal: Biochemistry / Year: 2016
Title: Metal-Dependent Function of a Mammalian Acireductone Dioxygenase.
Authors: Deshpande, A.R. / Wagenpfeil, K. / Pochapsky, T.C. / Petsko, G.A. / Ringe, D.
History
DepositionFeb 19, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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: 1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7293
Polymers21,5551
Non-polymers1752
Water3,801211
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.025, 79.025, 115.360
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein 1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase / Acireductone dioxygenase (Fe(2+)-requiring) / Fe-ARD / Membrane-type 1 matrix metalloproteinase ...Acireductone dioxygenase (Fe(2+)-requiring) / Fe-ARD / Membrane-type 1 matrix metalloproteinase cytoplasmic tail-binding protein 1 / MTCBP-1


Mass: 21554.574 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Adi1, Mtcbp1 / Plasmid: pMH4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL
References: UniProt: Q99JT9, acireductone dioxygenase [iron(II)-requiring]
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-69O / 2-oxopentanoic acid / 2-Ketopentanoic acid


Mass: 116.115 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / 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: 4.18 Å3/Da / Density % sol: 70.56 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 5.0% Glycerol, 19.0% iso-Propanol, 19.0% PEG-4000, 0.1M Citrate pH 5.6

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.23→50 Å / Num. obs: 18013 / % possible obs: 96.3 % / Redundancy: 26 % / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.016 / Rrim(I) all: 0.081 / Χ2: 1.034 / Net I/av σ(I): 43.5 / Net I/σ(I): 13.9 / Num. measured all: 469102
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.23-2.3117.70.311175.2
2.31-2.425.50.2761100
2.4-2.51260.2091100
2.51-2.6426.80.1661100
2.64-2.8127.50.1321100
2.81-3.0328.30.1031100
3.03-3.3328.20.0781100
3.33-3.8125.70.067187.3
3.81-4.827.30.061100
4.8-5025.20.047199.5

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.64 Å31.68 Å
Translation6.64 Å31.68 Å

-
Processing

Software
NameVersionClassification
SCALEPACKv705bdata scaling
PHASERv1.9phasing
PHENIXv1.9refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VR3

1vr3


Resolution: 2.236→31.678 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.03
RfactorNum. reflection% reflectionSelection details
Rfree0.2098 1786 10.01 %Random selection
Rwork0.1803 ---
obs0.1833 17844 97.45 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 76.54 Å2 / Biso mean: 29.3538 Å2 / Biso min: 14.28 Å2
Refinement stepCycle: final / Resolution: 2.236→31.678 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1484 0 16 211 1711
Biso mean--37.86 36.57 -
Num. residues----179
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071587
X-RAY DIFFRACTIONf_angle_d0.9532148
X-RAY DIFFRACTIONf_chiral_restr0.037221
X-RAY DIFFRACTIONf_plane_restr0.004278
X-RAY DIFFRACTIONf_dihedral_angle_d14.811610
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2359-2.29640.48881160.45641047116384
2.2964-2.36390.25711370.227212311368100
2.3639-2.44020.20841370.176712351372100
2.4402-2.52740.21861380.171612461384100
2.5274-2.62850.22361390.167712531392100
2.6285-2.74810.25331380.169412431381100
2.7481-2.89290.21051390.170612461385100
2.8929-3.0740.18661400.176612541394100
3.074-3.31110.21981400.177712691409100
3.3111-3.64390.17261310.1551161129299
3.6439-4.17010.20291310.16011178130992
4.1701-5.25010.13551440.144613071451100
5.2501-31.68070.21831560.186113881544100

+
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