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- PDB-2zzm: The complex structure of aTrm5 and tRNALeu -

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Basic information

Entry
Database: PDB / ID: 2zzm
TitleThe complex structure of aTrm5 and tRNALeu
Components
  • RNA (84-MER)
  • Uncharacterized protein MJ0883
KeywordsTRANSFERASE/RNA / protein-rna complex / TRANSFERASE-RNA COMPLEX
Function / homology
Function and homology information


tRNA methyltransferase activity / tRNA N1-guanine methylation / tRNA (guanine37-N1)-methyltransferase / tRNA (guanine(37)-N1)-methyltransferase activity / tRNA methylation / cytoplasm
Similarity search - Function
Alpha-Beta Plaits - #2580 / tRNA methyltransferase 5, N-terminal / tRNA methyltransferase 5 N-terminal domain / Met-10+ protein-like domains / SAM-dependent methyltransferase TRM5/TYW2-type domain profile. / SAM-dependent methyltransferase TRM5/TYW2-type / Met-10+ like-protein / GMP Synthetase; Chain A, domain 3 / Vaccinia Virus protein VP39 / Alpha-Beta Plaits ...Alpha-Beta Plaits - #2580 / tRNA methyltransferase 5, N-terminal / tRNA methyltransferase 5 N-terminal domain / Met-10+ protein-like domains / SAM-dependent methyltransferase TRM5/TYW2-type domain profile. / SAM-dependent methyltransferase TRM5/TYW2-type / Met-10+ like-protein / GMP Synthetase; Chain A, domain 3 / Vaccinia Virus protein VP39 / Alpha-Beta Plaits / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / : / RNA / RNA (> 10) / tRNA (guanine(37)-N1)-methyltransferase Trm5b
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsGoto-Ito, S. / Ito, T. / Yokoyama, S.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2009
Title: Tertiary structure checkpoint at anticodon loop modification in tRNA functional maturation
Authors: Goto-Ito, S. / Ito, T. / Kuratani, M. / Bessho, Y. / Yokoyama, S.
History
DepositionFeb 19, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 15, 2023Group: Advisory / Derived calculations
Category: ndb_struct_conf_na / ndb_struct_na_base_pair ...ndb_struct_conf_na / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_distant_solvent_atoms / pdbx_struct_conn_angle / struct_conn / struct_conn_type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein MJ0883
B: RNA (84-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,9738
Polymers67,4532
Non-polymers5206
Water70339
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4950 Å2
ΔGint-58 kcal/mol
Surface area27160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.399, 138.390, 61.654
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Uncharacterized protein MJ0883


Mass: 39124.023 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: Q58293
#2: RNA chain RNA (84-MER)


Mass: 28328.891 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: synthesized in vitro with the recombinant RNA polymerase of T7 phage
References: GenBank: 6626255
#3: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.39 %
Crystal growTemperature: 293 K / Method: sitting drop, vapor diffusion / pH: 7.2
Details: 175mM Mg(HCOO)2, 13% PEG 3350, 25mM KCl, 35mM Na-HEPES, pH 7.2, sitting drop, vapor diffusion, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1Mg(HCOO)211
2PEG 335011
3KCl11
4Na-HEPES11
5H2O11
6Mg(HCOO)212
7PEG 335012
8KCl12
9Na-HEPES12
10H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 19, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. obs: 20282 / Biso Wilson estimate: 70.8 Å2

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Processing

Software
NameVersionClassification
CNS1.2refinement
ADSCQuantumdata collection
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2yx1 and 1wz2

2yx1

1wz2


Resolution: 2.65→46.03 Å / Rfactor Rfree error: 0.009 / Occupancy max: 1 / Occupancy min: 1 / Data cutoff high absF: 1219642.89 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.289 1022 5.1 %RANDOM
Rwork0.215 ---
obs0.215 20064 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 73.3428 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 70.8 Å2
Baniso -1Baniso -2Baniso -3
1-16.99 Å20 Å20 Å2
2---14.78 Å20 Å2
3----2.21 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.68 Å0.48 Å
Refinement stepCycle: LAST / Resolution: 2.65→46.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2724 1793 32 39 4588
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
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_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.41
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it5.871.5
X-RAY DIFFRACTIONc_mcangle_it8.062
X-RAY DIFFRACTIONc_scbond_it8.482
X-RAY DIFFRACTIONc_scangle_it10.952.5
LS refinement shellResolution: 2.65→2.82 Å / Rfactor Rfree error: 0.039 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.51 172 5.3 %
Rwork0.402 3076 -
obs--98.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_mlz.paramprotein_mlz.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3adomet.paramwater.top
X-RAY DIFFRACTION4ion.paramadomet.top
X-RAY DIFFRACTION5water_rep.paramion.top

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