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- PDB-2zxu: Crystal structure of tRNA modification enzyme MiaA in the complex... -

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Basic information

Entry
Database: PDB / ID: 2zxu
TitleCrystal structure of tRNA modification enzyme MiaA in the complex with tRNA(Phe) and DMASPP
Components
  • tRNA delta(2)-isopentenylpyrophosphate transferase
  • tRNA(Phe)
KeywordsTRANSFERASE/RNA / PROTEIN-RNA COMPLEX / ATP-binding / tRNA modification enzyme / Nucleotide-binding / Nucleotidyltransferase / Transferase / tRNA processing / TRANSFERASE-RNA COMPLEX
Function / homology
Function and homology information


regulation of cytoplasmic translation in response to stress / tRNA dimethylallyltransferase / tRNA dimethylallyltransferase activity / tRNA modification / cellular response to heat / ATP binding
Similarity search - Function
IPP transferase / Dimethylallyltransferase / IPP transferase / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DIMETHYLALLYL S-THIOLODIPHOSPHATE / : / RNA / RNA (> 10) / tRNA dimethylallyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsSakai, J. / Yao, M. / Chimnaronk, S. / Tanaka, I.
CitationJournal: Biochemistry / Year: 2009
Title: Snapshots of dynamics in synthesizing N(6)-isopentenyladenosine at the tRNA anticodon
Authors: Chimnaronk, S. / Forouhar, F. / Sakai, J. / Yao, M. / Tron, C.M. / Atta, M. / Fontecave, M. / Hunt, J.F. / Tanaka, I.
History
DepositionJan 7, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 26, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Oct 16, 2019Group: Data collection / Non-polymer description / Structure summary
Category: chem_comp / entity
Item: _chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight
Revision 2.1Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_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: tRNA delta(2)-isopentenylpyrophosphate transferase
B: tRNA delta(2)-isopentenylpyrophosphate transferase
C: tRNA(Phe)
D: tRNA(Phe)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,95316
Polymers119,1854
Non-polymers76712
Water3,549197
1
A: tRNA delta(2)-isopentenylpyrophosphate transferase
C: tRNA(Phe)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,04911
Polymers59,5932
Non-polymers4579
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5500 Å2
ΔGint-92 kcal/mol
Surface area23690 Å2
MethodPISA
2
B: tRNA delta(2)-isopentenylpyrophosphate transferase
D: tRNA(Phe)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9035
Polymers59,5932
Non-polymers3113
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4850 Å2
ΔGint-45 kcal/mol
Surface area23390 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11700 Å2
ΔGint-149 kcal/mol
Surface area45720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.300, 90.000, 150.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein tRNA delta(2)-isopentenylpyrophosphate transferase / MiaA / IPP transferase / Isopentenyl-diphosphate:tRNA isopentenyltransferase / IPTase / IPPT


Mass: 35107.094 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: minaA / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P16384, EC: 2.5.1.8
#2: RNA chain tRNA(Phe)


Mass: 24485.539 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: tRNA(Phe) was prepared by in vitro transcription. This sequence occurs naturally in Escherichia coli St.K12.
Source: (synth.) Escherichia coli (E. coli) / References: GenBank: 169887498
#3: Chemical ChemComp-DST / DIMETHYLALLYL S-THIOLODIPHOSPHATE / DMASPP / DMAPP / DMADP / Dimethylallyl pyrophosphate / dimethylallyl diphosphate / isoprenyl pyrophosphate


Mass: 262.158 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H12O6P2S
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 2.51 Å3/Da / Density % sol: 50.97 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 0.09M MES, 24% PEG 3350, 0.18mM Ca(OAc)2, 0.01mM tri-Sodium Citrate dihydrate pH 5.6, 2% iso-Propanol, 2% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Components of the solutions
IDNameCrystal-IDSol-ID
1MES11
2PEG 335011
3Ca(OAc)211
4tri-Sodium Citrate dihydrate11
5iso-Propanol11
6PEG 400011
7H2O11
8MES12
9PEG 335012
10Ca(OAc)212
11tri-Sodium Citrate dihydrate12
12PEG 400012
13H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 3, 2007 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. obs: 31721 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Net I/σ(I): 16.8
Reflection shellResolution: 2.75→2.85 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.368 / Mean I/σ(I) obs: 6 / Num. unique all: 3111 / Rsym value: 0.368 / % possible all: 99.8

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Processing

Software
NameVersionClassification
LAFIREmodel building
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
LAFIREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ZM5

2zm5


Resolution: 2.75→20 Å / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: LAFIRE was also used in refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.281 2211 7 %RANDOM
Rwork0.237 ---
all-31721 --
obs-31721 99.8 %-
Displacement parametersBiso max: 90 Å2 / Biso mean: 41.97 Å2 / Biso min: 10 Å2
Baniso -1Baniso -2Baniso -3
1-1.247 Å20 Å20 Å2
2---9.8 Å20 Å2
3---8.554 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.4 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.75→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4800 3046 38 197 8081
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.33
X-RAY DIFFRACTIONc_dihedral_angle_d21.22
X-RAY DIFFRACTIONc_improper_angle_d1.47
LS refinement shellResolution: 2.75→2.85 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.3645 236 7.5 %
Rwork0.3169 2900 -
obs-3136 99.8 %

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