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- PDB-2der: Cocrystal structure of an RNA sulfuration enzyme MnmA and tRNA-Gl... -

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Basic information

Entry
Database: PDB / ID: 2der
TitleCocrystal structure of an RNA sulfuration enzyme MnmA and tRNA-Glu in the initial tRNA binding state
Components
  • tRNA
  • tRNA-specific 2-thiouridylase mnmA
KeywordsTransferase/RNA / Protein-RNA complex / Transferase-RNA COMPLEX
Function / homology
Function and homology information


tRNA-uridine 2-sulfurtransferase / sulfurtransferase complex / tRNA wobble position uridine thiolation / sulfurtransferase activity / tRNA binding / ATP binding / cytosol
Similarity search - Function
tRNA-specific 2-thiouridylase MnmA-like, central domain / tRNA-specific 2-thiouridylase MnmA-like, C-terminal domain / tRNA methyl transferase HUP domain / Aminomethyltransferase beta-barrel domain / tRNA methyl transferase PRC-barrel domain / Adenine nucleotide alpha hydrolases-like domains / tRNA-specific 2-thiouridylase / tRNA-specific 2-thiouridylase MnmA-like, central domain superfamily / Translation factors / HUPs ...tRNA-specific 2-thiouridylase MnmA-like, central domain / tRNA-specific 2-thiouridylase MnmA-like, C-terminal domain / tRNA methyl transferase HUP domain / Aminomethyltransferase beta-barrel domain / tRNA methyl transferase PRC-barrel domain / Adenine nucleotide alpha hydrolases-like domains / tRNA-specific 2-thiouridylase / tRNA-specific 2-thiouridylase MnmA-like, central domain superfamily / Translation factors / HUPs / Elongation Factor Tu (Ef-tu); domain 3 / Rossmann-like alpha/beta/alpha sandwich fold / SH3 type barrels. / Roll / Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / RNA / RNA (> 10) / tRNA-specific 2-thiouridylase MnmA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsNumata, T. / Ikeuchi, Y. / Fukai, S. / Suzuki, T. / Nureki, O.
CitationJournal: Nature / Year: 2006
Title: Snapshots of tRNA sulphuration via an adenylated intermediate
Authors: Numata, T. / Ikeuchi, Y. / Fukai, S. / Suzuki, T. / Nureki, O.
History
DepositionFeb 17, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 15, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 / _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
C: tRNA
D: tRNA
A: tRNA-specific 2-thiouridylase mnmA
B: tRNA-specific 2-thiouridylase mnmA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,44113
Polymers133,5814
Non-polymers8609
Water00
1
C: tRNA
A: tRNA-specific 2-thiouridylase mnmA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,2687
Polymers66,7902
Non-polymers4785
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: tRNA
B: tRNA-specific 2-thiouridylase mnmA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,1726
Polymers66,7902
Non-polymers3824
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)225.389, 175.845, 52.965
Angle α, β, γ (deg.)90.00, 101.62, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: RNA chain tRNA


Mass: 24378.514 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: RNA was prepared by in vitro transcription.
#2: Protein tRNA-specific 2-thiouridylase mnmA / RNA sulfuration enzyme MnmA


Mass: 42411.816 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pQE80L / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)
References: UniProt: P25745, Transferases; Transferring sulfur-containing groups; Sulfurtransferases
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4

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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: 3.85 Å3/Da / Density % sol: 68.03 %
Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 90mM HEPES-Na buffer (pH 7.5), 40mM ammonium dihydrogen phosphate, 1.8% PEG400, 1.7-1.9M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG40011
2HEPES-Na11
3ammonium dihydrogen phosphate11
4ammonium sulfate11
5HOH11
6PEG40012
7HEPES-Na12
8ammonium dihydrogen phosphate12
9ammonium sulfate12
10HOH12

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Data collection

DiffractionMean temperature: 30 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.97927 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 7, 2004
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97927 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 61680 / % possible obs: 89.8 % / Redundancy: 4.3 % / Biso Wilson estimate: 0 Å2 / Rmerge(I) obs: 0.118 / Net I/σ(I): 11.2
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.363 / Mean I/σ(I) obs: 1.8 / % possible all: 41.9

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2DET

2det


Resolution: 3.1→46.75 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 75333.9 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS.
RfactorNum. reflection% reflectionSelection details
Rfree0.269 2901 4.8 %RANDOM
Rwork0.219 ---
obs0.219 60663 83.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 24.9515 Å2 / ksol: 0.283117 e/Å3
Displacement parametersBiso mean: 69 Å2
Baniso -1Baniso -2Baniso -3
1-5.32 Å20 Å212.37 Å2
2---5.58 Å20 Å2
3---0.25 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.51 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.85 Å0.8 Å
Refinement stepCycle: LAST / Resolution: 3.1→46.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5548 3082 45 0 8675
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.3
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3.1→3.29 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.422 187 4.1 %
Rwork0.388 4404 -
obs--38.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3ion.paramion.top

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