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- PDB-1vr3: Crystal structure of Acireductone dioxygenase (13543033) from Mus... -

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Basic information

Entry
Database: PDB / ID: 1vr3
TitleCrystal structure of Acireductone dioxygenase (13543033) from Mus musculus at 2.06 A resolution
ComponentsAcireductone dioxygenase
KeywordsOXIDOREDUCTASE / 13543033 / ACIREDUCTONE DIOXYGENASE / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI
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
ISOPROPYL ALCOHOL / NICKEL (II) ION / Unknown ligand / Acireductone dioxygenase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.06 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: Proteins / Year: 2006
Title: Crystal structure of acireductone dioxygenase (ARD) from Mus musculus at 2.06 angstrom resolution.
Authors: Xu, Q. / Schwarzenbacher, R. / Krishna, S.S. / McMullan, D. / Agarwalla, S. / Quijano, K. / Abdubek, P. / Ambing, E. / Axelrod, H. / Biorac, T. / Canaves, J.M. / Chiu, H.J. / Elsliger, M.A. ...Authors: Xu, Q. / Schwarzenbacher, R. / Krishna, S.S. / McMullan, D. / Agarwalla, S. / Quijano, K. / Abdubek, P. / Ambing, E. / Axelrod, H. / Biorac, T. / Canaves, J.M. / Chiu, H.J. / Elsliger, M.A. / Grittini, C. / Grzechnik, S.K. / DiDonato, M. / Hale, J. / Hampton, E. / Han, G.W. / Haugen, J. / Hornsby, M. / Jaroszewski, L. / Klock, H.E. / Knuth, M.W. / Koesema, E. / Kreusch, A. / Kuhn, P. / Miller, M.D. / Moy, K. / Nigoghossian, E. / Paulsen, J. / Reyes, R. / Rife, C. / Spraggon, G. / Stevens, R.C. / van den Bedem, H. / Velasquez, J. / White, A. / Wolf, G. / Hodgson, K.O. / Wooley, J. / Deacon, A.M. / Godzik, A. / Lesley, S.A. / Wilson, I.A.
History
DepositionJan 28, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acireductone dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6044
Polymers23,4851
Non-polymers1193
Water3,045169
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.136, 79.136, 114.128
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Acireductone dioxygenase


Mass: 23485.158 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
References: UniProt: Q99JT9, Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of two atoms of oxygen
#2: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#4: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 3.71 Å3/Da / Density % sol: 66.57 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 5.6
Details: 5.0% Glycerol, 19.0% iso-Propanol, 19.0% PEG-4000, 0.1M Citrate pH 5.6, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.979735,0.979562,0.956885
DetectorType: ADSC / Detector: CCD / Date: Nov 10, 2004 / Details: fixed-height exit beam, toroidal focusing mirror
RadiationMonochromator: Double-crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9797351
20.9795621
30.9568851
ReflectionResolution: 2.06→28.54 Å / Num. obs: 23148 / % possible obs: 100 % / Redundancy: 6.8 % / Biso Wilson estimate: 43.37 Å2 / Rsym value: 0.101 / Net I/σ(I): 13.6
Reflection shellResolution: 2.06→2.17 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 3314 / Rsym value: 0.864 / % possible all: 100

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Processing

Software
NameVersionClassification
XDSdata scaling
SCALA5.0)data scaling
autoSHARPphasing
REFMAC5.2.0005refinement
XDSdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.06→28.53 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.949 / SU B: 5.439 / SU ML: 0.081 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.115
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. THE IDENTITY OF THE METAL BOUND IS UNKNOWN. IT WAS TENTATIVELY ASSIGNED AS A NICKLE. BASED ON INFORMATION OF HOMOLOGOUS PROTEINS, IT ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. THE IDENTITY OF THE METAL BOUND IS UNKNOWN. IT WAS TENTATIVELY ASSIGNED AS A NICKLE. BASED ON INFORMATION OF HOMOLOGOUS PROTEINS, IT COULD BE NI2+ OR FE2+. HOWEVER, IT COULD BE ALSO OTHER METALS. 3. SUSPICIOUS DENSITIES: NEAR THR11, IT WAS MODELLED AS A WATER WAT136; ANOTHER DENSITY IN THE ACTIVE SITE WAS MODELLED AS UNKNOWN LIGAND, UNL. THE UNL INTERACTS WITH THE UNKNOWN METAL.
RfactorNum. reflection% reflectionSelection details
Rfree0.19532 1183 5.1 %RANDOM
Rwork0.16229 ---
obs0.16387 21908 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 37.722 Å2
Baniso -1Baniso -2Baniso -3
1--0.48 Å20 Å20 Å2
2---0.48 Å20 Å2
3---0.96 Å2
Refinement stepCycle: LAST / Resolution: 2.06→28.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1484 0 14 169 1667
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221583
X-RAY DIFFRACTIONr_bond_other_d0.0020.021421
X-RAY DIFFRACTIONr_angle_refined_deg1.4361.9492143
X-RAY DIFFRACTIONr_angle_other_deg0.79933295
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4255178
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.21623.18288
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.93515284
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.4331516
X-RAY DIFFRACTIONr_chiral_restr0.0830.2221
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021729
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02346
X-RAY DIFFRACTIONr_nbd_refined0.2140.2293
X-RAY DIFFRACTIONr_nbd_other0.1960.21423
X-RAY DIFFRACTIONr_nbtor_other0.0850.2919
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2020.2140
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1070.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.250.224
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1530.25
X-RAY DIFFRACTIONr_mcbond_it2.8873940
X-RAY DIFFRACTIONr_mcbond_other0.63357
X-RAY DIFFRACTIONr_mcangle_it3.50451479
X-RAY DIFFRACTIONr_scbond_it6.0338761
X-RAY DIFFRACTIONr_scangle_it8.38211664
X-RAY DIFFRACTIONr_nbtor_refined0.1880.2758
LS refinement shellResolution: 2.06→2.114 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 91 5.43 %
Rwork0.243 1585 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 45.816 Å / Origin y: 14.8274 Å / Origin z: 49.5691 Å
111213212223313233
T-0.1005 Å20.0133 Å20.0167 Å2--0.0814 Å2-0.0269 Å2---0.0741 Å2
L2.4355 °2-0.1448 °2-1.1836 °2-0.8176 °20.2589 °2--1.8039 °2
S0.003 Å °-0.0569 Å °-0.0636 Å °0.0065 Å °0.0336 Å °-0.0037 Å °-0.0112 Å °0.1229 Å °-0.0366 Å °
Refinement TLS groupSelection: ALL

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