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- PDB-4qgn: Human acireductone dioxygenase with iron ion and L-methionine in ... -

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Basic information

Entry
Database: PDB / ID: 4qgn
TitleHuman acireductone dioxygenase with iron ion and L-methionine in active center
Components1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase
KeywordsOXIDOREDUCTASE / RmlC-like cupin / Iron Binding / 1 / 2-dihydroxy-5-(methylthio)pent-1-en-3-one dioxygenase
Function / homology
Function and homology information


acireductone dioxygenase (Ni2+-requiring) / acireductone dioxygenase [iron(II)-requiring] / acireductone dioxygenase (Ni2+-requiring) activity / acireductone dioxygenase [iron(II)-requiring] activity / Methionine salvage pathway / methionine metabolic process / L-methionine salvage from methylthioadenosine / nickel cation binding / oxidoreductase activity / iron ion binding ...acireductone dioxygenase (Ni2+-requiring) / acireductone dioxygenase [iron(II)-requiring] / acireductone dioxygenase (Ni2+-requiring) activity / acireductone dioxygenase [iron(II)-requiring] activity / Methionine salvage pathway / methionine metabolic process / L-methionine salvage from methylthioadenosine / nickel cation binding / oxidoreductase activity / iron ion binding / nucleus / plasma membrane / cytosol / 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
ACETATE ION / : / SELENOMETHIONINE / Acireductone dioxygenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å
AuthorsMilaczewska, A.M. / Chruszcz, M. / Petkowski, J.J. / Niedzialkowska, E. / Minor, W. / Borowski, T.
CitationJournal: Chemistry / Year: 2018
Title: On the Structure and Reaction Mechanism of Human Acireductone Dioxygenase.
Authors: Milaczewska, A. / Kot, E. / Amaya, J.A. / Makris, T.M. / Zajac, M. / Korecki, J. / Chumakov, A. / Trzewik, B. / Kedracka-Krok, S. / Minor, W. / Chruszcz, M. / Borowski, T.
History
DepositionMay 23, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.2Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 9, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.4Sep 20, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.5Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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)22,56710
Polymers21,8011
Non-polymers7669
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)105.195, 105.195, 40.822
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 21800.697 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADI1, HMFT1638, MTCBP1, NP_060739 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CodonPlus DE3 RIPL
References: UniProt: Q9BV57, acireductone dioxygenase [iron(II)-requiring]

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Non-polymers , 6 types, 35 molecules

#2: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-MSE / SELENOMETHIONINE / Selenomethionine


Type: L-peptide linking / Mass: 196.106 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO2Se
#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.99 Å3/Da / Density % sol: 58.87 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: Protein: 20 mg/ml in 50 mM Tris-HCl pH 7.8, 150mM NaCl, 2.5mM L-selenomethionine, Crystallization condition: 0.1M sodium acetate, ammonium sulfate pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97912 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 22, 2012
Details: Rosenbaum-Rock vertical focusing mirror, with Pt, glass, Pd lanes
RadiationMonochromator: Rosenbaum-Rock high-resolution double-crystal monochromator. LN2 cooled first crystal, sagittal focusing 2nd crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97912 Å / Relative weight: 1
ReflectionResolution: 3.05→50 Å / Num. all: 5073 / Num. obs: 5073 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.1 % / Rmerge(I) obs: 0.182 / Rsym value: 0.182 / Net I/σ(I): 11.037
Reflection shellResolution: 3.05→3.1 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.726 / Mean I/σ(I) obs: 2.118 / Rsym value: 0.726 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-3000data collection
DENZO3000: MOLREPdata reduction
SCALEPACK3000: MOLREPdata scaling
REFMAC5.6.0117refinement
Cootmodel building
HKL-3000phasing
CCP4refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1vr3

1vr3


Resolution: 3.05→37.25 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.89 / SU B: 33.496 / SU ML: 0.287 / Cross valid method: THROUGHOUT / ESU R Free: 0.401 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2279 232 4.6 %RANDOM
Rwork0.17753 ---
obs0.17994 4829 99.72 %-
all-4829 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.363 Å2
Baniso -1Baniso -2Baniso -3
1--3.22 Å2-1.61 Å20 Å2
2---3.22 Å20 Å2
3---4.84 Å2
Refinement stepCycle: LAST / Resolution: 3.05→37.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1487 0 36 26 1549
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.021570
X-RAY DIFFRACTIONr_bond_other_d0.0030.021090
X-RAY DIFFRACTIONr_angle_refined_deg1.2761.972120
X-RAY DIFFRACTIONr_angle_other_deg0.83632617
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6295177
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.54423.05985
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.61115253
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4451515
X-RAY DIFFRACTIONr_chiral_restr0.0640.2212
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211726
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02352
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.052→3.131 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 16 -
Rwork0.257 333 -
obs--99.15 %
Refinement TLS params.Method: refined / Origin x: 23.8444 Å / Origin y: -27.0129 Å / Origin z: -0.4558 Å
111213212223313233
T0.0486 Å20.0039 Å2-0.0077 Å2-0.0071 Å2-0.0093 Å2--0.0329 Å2
L1.5779 °20.3508 °2-0.1791 °2-1.5831 °20.0794 °2--0.5637 °2
S0.0194 Å °-0.0172 Å °0.0348 Å °-0.1248 Å °-0.0603 Å °0.0809 Å °-0.0217 Å °-0.0513 Å °0.0409 Å °

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