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- PDB-5i93: Structure of Mouse Acireductone dioxygenase with Ni2+ and 2-ketop... -

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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 / methionine metabolic process / L-methionine salvage from methylthioadenosine / nickel cation binding / oxidoreductase activity / iron ion binding ...Methionine salvage pathway / acireductone dioxygenase (Ni2+-requiring) / acireductone dioxygenase [iron(II)-requiring] / acireductone dioxygenase (Ni2+-requiring) activity / acireductone dioxygenase [iron(II)-requiring] activity / methionine metabolic process / 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

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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)21,7293
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

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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 / 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

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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: 70.56 %
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

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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

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Phasing

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

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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

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