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- PDB-6zma: Structure of the tRNA-Monooxygenase enzyme MiaE frozen under 140 ... -

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Basic information

Entry
Database: PDB / ID: 6zma
TitleStructure of the tRNA-Monooxygenase enzyme MiaE frozen under 140 bar of krypton using the soak and freeze methodology
ComponentstRNA hydroxylase
KeywordsOXIDOREDUCTASE / tRNA-monooxygenase metallo-enzyme tRNA-modifying enzyme hydroxylase
Function / homology
Function and homology information


tRNA 2-(methylsulfanyl)-N(6)-isopentenyladenosine(37) hydroxylase activity / tRNA modification / metal ion binding
Similarity search - Function
tRNA-hydroxylase MiaE / tRNA-(MS[2]IO[6]A)-hydroxylase (MiaE) / Ferritin-like / Ferritin-like superfamily
Similarity search - Domain/homology
: / KRYPTON / DI(HYDROXYETHYL)ETHER / tRNA-(Ms[2]io[6]A)-hydroxylase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsCarpentier, P. / Atta, M.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-15-CE21-0020 France
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: Structural, biochemical and functional analyses of tRNA-monooxygenase enzyme MiaE from Pseudomonas putida provide insights into tRNA/MiaE interaction.
Authors: Carpentier, P. / Lepretre, C. / Basset, C. / Douki, T. / Torelli, S. / Duarte, V. / Hamdane, D. / Fontecave, M. / Atta, M.
History
DepositionJul 2, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 2, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 31, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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
B: tRNA hydroxylase
C: tRNA hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,44728
Polymers46,2372
Non-polymers2,20926
Water3,819212
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7840 Å2
ΔGint-44 kcal/mol
Surface area16470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.622, 52.300, 79.407
Angle α, β, γ (deg.)90.000, 90.740, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-305-

CA

21B-421-

HOH

31B-444-

HOH

41B-479-

HOH

51B-480-

HOH

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Components

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Protein , 1 types, 2 molecules BC

#1: Protein tRNA hydroxylase / tRNA-(MS[2]IO[6]A)-hydroxylase (MiaE) / tRNA-(Ms[2]io[6]A)-hydroxylase


Mass: 23118.668 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: AYO08_21560, CBL13_00280, CBP06_18695 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: A0A179QS89

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Non-polymers , 9 types, 238 molecules

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


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#8: Chemical
ChemComp-KR / KRYPTON


Mass: 83.798 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Kr / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.71 Å3/Da / Density % sol: 54.58 % / Description: elongated
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8
Details: MiaE:20 mg/ml in 100 mM HEPES, pH 7.5, 30 mM NaCl reservoir solution: 0.5 M CaCl2, 42% PEG 6k, 2 M Tris-Cl pH 8 frozen under 140 bar of krypton Krypton atoms were located in anomalous map

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.861 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 31, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.861 Å / Relative weight: 1
ReflectionResolution: 2.15→80 Å / Num. obs: 25240 / % possible obs: 94.6 % / Observed criterion σ(I): 1.4 / Redundancy: 6.1 % / Biso Wilson estimate: 48.7 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.076 / Net I/σ(I): 15.7
Reflection shellResolution: 2.15→2.28 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 3108 / CC1/2: 0.69 / Rrim(I) all: 0.095 / % possible all: 72.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ITB

2itb


Resolution: 2.15→79.4 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.937 / SU B: 6.535 / SU ML: 0.159 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.234 / ESU R Free: 0.206 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY KR atoms (low occupancies) have been located in anomalous map
RfactorNum. reflection% reflectionSelection details
Rfree0.2439 1290 5.1 %RANDOM
Rwork0.1796 ---
obs0.1828 23939 94.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 118.02 Å2 / Biso mean: 48.887 Å2 / Biso min: 27.93 Å2
Baniso -1Baniso -2Baniso -3
1--2.27 Å20 Å2-1.51 Å2
2--0.92 Å2-0 Å2
3---1.39 Å2
Refinement stepCycle: final / Resolution: 2.15→79.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3131 0 101 212 3444
Biso mean--67.58 58.89 -
Num. residues----398
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0193288
X-RAY DIFFRACTIONr_bond_other_d0.0020.023234
X-RAY DIFFRACTIONr_angle_refined_deg1.4351.994425
X-RAY DIFFRACTIONr_angle_other_deg0.97737403
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4895406
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.15222.897145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.03815547
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0031531
X-RAY DIFFRACTIONr_chiral_restr0.0740.2492
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213643
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02736
LS refinement shellResolution: 2.15→2.202 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.366 67 -
Rwork0.32 1185 -
obs--64.44 %

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