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- PDB-5i91: Structure of Mouse Acirecutone dioxygenase with to Ni2+ and 2-ket... -

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Basic information

Entry
Database: PDB / ID: 5i91
TitleStructure of Mouse Acirecutone dioxygenase with to Ni2+ and 2-keto-4-(methylthio)-butyric acid in the active site
Components1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase
KeywordsOXIDOREDUCTASE / 2-keto-4-(methylthio)-butyric 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
4-(METHYLSULFANYL)-2-OXOBUTANOIC ACID / NICKEL (II) ION / Acireductone dioxygenase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.76 Å
AuthorsDeshpande, A.R. / Robinson, H. / 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

Downloads & links

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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)21,7613
Polymers21,5551
Non-polymers2072
Water4,810267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.185, 79.185, 114.576
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 strain
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-KMT / 4-(METHYLSULFANYL)-2-OXOBUTANOIC ACID


Mass: 148.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H8O3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / 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: 4.17 Å3/Da / Density % sol: 70.48 %
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: Sep 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.76→50 Å / Num. obs: 36891 / % possible obs: 100 % / Redundancy: 29.4 % / Biso Wilson estimate: 24.35 Å2 / Rmerge(I) obs: 0.086 / Net I/av σ(I): 50.023 / Net I/σ(I): 9.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.76-1.8225.90.8691100
1.82-1.928.60.6211100
1.9-1.9828.80.4151100
1.98-2.0928.80.2851100
2.09-2.2228.90.1921100
2.22-2.3928.80.1431100
2.39-2.6328.70.0981100
2.63-3.0128.50.0721100
3.01-3.79280.0631100
3.79-5037.90.0641100

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.64 Å46.41 Å
Translation6.64 Å46.41 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: 1.76→46.415 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.29
RfactorNum. reflection% reflectionSelection details
Rfree0.1994 3736 5.41 %Random slection
Rwork0.1729 ---
obs0.1743 36823 99.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 79.47 Å2 / Biso mean: 29.0253 Å2 / Biso min: 15.32 Å2
Refinement stepCycle: final / Resolution: 1.76→46.415 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1484 0 17 267 1768
Biso mean--37.67 37.88 -
Num. residues----179
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071588
X-RAY DIFFRACTIONf_angle_d1.0142149
X-RAY DIFFRACTIONf_chiral_restr0.041221
X-RAY DIFFRACTIONf_plane_restr0.005278
X-RAY DIFFRACTIONf_dihedral_angle_d15.407611
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.7598-1.78210.28631370.274123892526
1.7821-1.80550.27831380.244324252563
1.8055-1.83030.24761420.225524132555
1.8303-1.85640.21981360.216524262562
1.8564-1.88410.22061420.214524382580
1.8841-1.91360.2611320.191723742506
1.9136-1.9450.23671380.195424272565
1.945-1.97850.1661450.191924352580
1.9785-2.01450.25161400.177624052545
2.0145-2.05320.21221370.177524252562
2.0532-2.09510.17121330.175423862519
2.0951-2.14070.20271390.182924502589
2.1407-2.19050.2061430.171324222565
2.1905-2.24530.21741360.188524352571
2.2453-2.3060.19591320.181223872519
2.306-2.37380.21841440.180524212565
2.3738-2.45040.22041390.180724112550
2.4504-2.5380.19071410.182124222563
2.538-2.63960.20361350.180924462581
2.6396-2.75970.17411400.167123882528
2.7597-2.90520.1961380.17824222560
2.9052-3.08720.21571400.176624172557
3.0872-3.32550.19251350.181824272562
3.3255-3.660.18021380.156924152553
3.66-4.18940.18371390.151924182557
4.1894-5.2770.2081400.132824272567
5.277-46.43080.17181370.176124132550

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