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- PDB-5i8s: Structure of Mouse Acireductone dioxygenase with Ni2+ ion and pen... -

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Basic information

Entry
Database: PDB / ID: 5i8s
TitleStructure of Mouse Acireductone dioxygenase with Ni2+ ion and pentanoic acid in the active site
Components1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase
KeywordsOXIDOREDUCTASE / Product analog / off-pathway chemistry
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
PENTANOIC ACID / NICKEL (II) ION / Acireductone dioxygenase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7153
Polymers21,5551
Non-polymers1612
Water4,882271
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.090, 79.090, 115.355
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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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 / 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-LEA / PENTANOIC ACID / VALERIC ACID


Mass: 102.132 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H10O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 271 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 4.18 Å3/Da / Density % sol: 70.61 %
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.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.89→50 Å / Num. obs: 29822 / % possible obs: 99.3 % / Redundancy: 26 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 27.09
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.89-1.9625.30.7631100
1.96-2.04280.5471100
2.04-2.13280.3751100
2.13-2.2423.90.332198.9
2.24-2.3823.80.267199.1
2.38-2.5727.60.1621100
2.57-2.8227.20.1131100
2.82-3.2327.40.0791100
3.23-4.07230.062195.8
4.07-5025.60.049199.4

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Processing

Software
NameVersionClassification
HKL-2000v705bdata scaling
PHENIXv1.9refinement
PDB_EXTRACT3.2data extraction
HKL-2000c705bdata reduction
PHENIXv1.9phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VR3

1vr3


Resolution: 1.89→27.151 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.54
RfactorNum. reflection% reflection
Rfree0.2004 2000 5.36 %
Rwork0.1726 --
obs0.174 25886 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 74.67 Å2 / Biso mean: 28.1537 Å2 / Biso min: 13.31 Å2
Refinement stepCycle: final / Resolution: 1.89→27.151 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1484 0 17 271 1772
Biso mean--36.5 41.38 -
Num. residues----179
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071586
X-RAY DIFFRACTIONf_angle_d0.9672146
X-RAY DIFFRACTIONf_chiral_restr0.041221
X-RAY DIFFRACTIONf_plane_restr0.004277
X-RAY DIFFRACTIONf_dihedral_angle_d14.348610
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8905-1.93780.4611340.44031917205198
1.9378-1.99010.27641400.26441936207699
1.9901-2.04870.22841400.193319502090100
2.0487-2.11480.20651430.188119762119100
2.1148-2.19030.23111410.183319682109100
2.1903-2.2780.3511370.28671886202396
2.278-2.38160.23021400.21691957209799
2.3816-2.50710.2251430.181319762119100
2.5071-2.6640.21251410.178419792120100
2.664-2.86950.18531460.171320042150100
2.8695-3.15790.20531440.166220062150100
3.1579-3.61390.19511390.15321922206195
3.6139-4.54970.15021450.13752019216499
4.5497-27.17830.15421560.15621772333100

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