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- PDB-6zmc: Structure of the tRNA-Monooxygenase enzyme MiaE frozen under 2000... -

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Basic information

Entry
Database: PDB / ID: 6zmc
TitleStructure of the tRNA-Monooxygenase enzyme MiaE frozen under 2000 bar using the high pressure freezing method
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
ARGON / : / DI(HYDROXYETHYL)ETHER / tRNA-(Ms[2]io[6]A)-hydroxylase
Similarity search - Component
Biological speciesPseudomonas putida KT2440 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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

Downloads & links

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Assembly

Deposited unit
B: tRNA hydroxylase
C: tRNA hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,44015
Polymers45,3222
Non-polymers1,11813
Water93752
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4840 Å2
ΔGint-73 kcal/mol
Surface area17390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.388, 51.909, 78.978
Angle α, β, γ (deg.)90.000, 90.360, 90.000
Int Tables number5
Space group name H-MC121

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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: 22661.078 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida KT2440 (bacteria) / Gene: AYO08_21560, CBL13_00280, CBP06_18695 / Plasmid: synthetic plasmid pET28a-MiaE / Details (production host): kanamycin-resistant / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: A0A179QS89

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Non-polymers , 8 types, 65 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-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Chemical ChemComp-AR / ARGON


Mass: 39.948 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ar
#8: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.66 Å3/Da / Density % sol: 53.75 % / Description: elongated
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8
Details: protein : 20 mg/ml in 100 mM HEPES, pH 7.5, 30 mM NaCl reservoir : 0.5 M CaCl2, 42% PEG 6k, 2 M Tris-Cl pH 8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 1.77 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.77 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 16699 / % possible obs: 99.3 % / Observed criterion σ(I): 2.2 / Redundancy: 6.2 % / Biso Wilson estimate: 72.2 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.065 / Net I/σ(I): 16.5
Reflection shellResolution: 2.5→2.65 Å / Redundancy: 6.01 % / Mean I/σ(I) obs: 2.24 / Num. unique obs: 2618 / CC1/2: 0.912 / Rrim(I) all: 0.79 / % possible all: 97.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ITB

2itb


Resolution: 2.5→47.52 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.946 / SU B: 12.289 / SU ML: 0.259 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.47 / ESU R Free: 0.279 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2446 829 5 %RANDOM
Rwork0.1817 ---
obs0.1849 15868 99.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 144.51 Å2 / Biso mean: 69.561 Å2 / Biso min: 47.47 Å2
Baniso -1Baniso -2Baniso -3
1--5.55 Å20 Å2-3.97 Å2
2--2.01 Å2-0 Å2
3---3.59 Å2
Refinement stepCycle: final / Resolution: 2.5→47.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3155 0 57 52 3264
Biso mean--93.27 73.48 -
Num. residues----399
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0133199
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173023
X-RAY DIFFRACTIONr_angle_refined_deg1.4431.6344335
X-RAY DIFFRACTIONr_angle_other_deg1.251.5676942
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8165409
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.74220.602166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.55715498
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6591529
X-RAY DIFFRACTIONr_chiral_restr0.060.2412
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023612
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02685
LS refinement shellResolution: 2.5→2.56 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.325 67 -
Rwork0.314 1131 -
obs--95 %

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