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- PDB-2zm5: Crystal structure of tRNA modification enzyme MiaA in the complex... -

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Basic information

Entry
Database: PDB / ID: 2zm5
TitleCrystal structure of tRNA modification enzyme MiaA in the complex with tRNA(Phe)
Components
  • tRNA delta(2)-isopentenylpyrophosphate transferase
  • tRNA(Phe)
KeywordsTRANSFERASE/RNA / PROTEIN-RNA COMPLEX / 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 / AMP dimethylallyltransferase activity / tRNA modification / cellular response to heat / ATP binding
Similarity search - Function
Histone, subunit A - #140 / IPP transferase / Dimethylallyltransferase / IPP transferase / Histone, subunit A / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich ...Histone, subunit A - #140 / IPP transferase / Dimethylallyltransferase / IPP transferase / Histone, subunit A / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / RNA / RNA (> 10) / tRNA dimethylallyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Escherichia coli K12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.55 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
DepositionApr 11, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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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)120,10611
Polymers119,9364
Non-polymers1707
Water2,918162
1
A: tRNA delta(2)-isopentenylpyrophosphate transferase
C: tRNA(Phe)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,1148
Polymers59,9682
Non-polymers1466
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4580 Å2
ΔGint-72 kcal/mol
Surface area24040 Å2
MethodPISA
2
B: tRNA delta(2)-isopentenylpyrophosphate transferase
D: tRNA(Phe)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9923
Polymers59,9682
Non-polymers241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4030 Å2
ΔGint-34 kcal/mol
Surface area23680 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10000 Å2
ΔGint-119 kcal/mol
Surface area46330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.200, 89.400, 150.800
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 / IPP transferase / Isopentenyl-diphosphate:tRNA isopentenyltransferase / IPTase / IPPT


Mass: 35482.258 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: miaA / 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. / Source: (synth.) Escherichia coli K12 (bacteria) / References: GenBank: 169887498
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 2.48 Å3/Da / Density % sol: 50.37 %
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, pH 5.8, 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: SPring-8 / Beamline: BL41XU / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 14, 2006 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. all: 39165 / Num. obs: 39165 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Biso Wilson estimate: 64.2 Å2 / Rmerge(I) obs: 0.076 / Rsym value: 0.076 / Net I/σ(I): 21.9
Reflection shellResolution: 2.55→2.64 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 3.85 / Rsym value: 0.26 / % possible all: 93.6

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Processing

Software
NameVersionClassification
SHELXDphasing
SOLVEphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.55→20 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.27 2753 7 %RANDOM
Rwork0.24 ---
obs0.24 39165 99 %-
all-39098 --
Displacement parametersBiso mean: 58.87 Å2
Baniso -1Baniso -2Baniso -3
1-0.662 Å20 Å20 Å2
2---21.578 Å20 Å2
3---20.916 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.46 Å0.44 Å
Refinement stepCycle: LAST / Resolution: 2.55→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4800 3046 7 162 8015
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
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_deg1.72
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.64
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.75
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.17
X-RAY DIFFRACTIONc_mcangle_it1.986
X-RAY DIFFRACTIONc_scbond_it1.669
X-RAY DIFFRACTIONc_scangle_it2.537
LS refinement shellResolution: 2.55→2.64 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.3797 265 6.8 %
Rwork0.3558 3330 -
obs--92.61 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4dna-rna.paramdna-rna.top

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