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- PDB-2dr5: Complex structure of CCA adding enzyme with mini-helix lacking CCA -

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Basic information

Entry
Database: PDB / ID: 2dr5
TitleComplex structure of CCA adding enzyme with mini-helix lacking CCA
Components
  • CCA-adding enzyme
  • tRNA (32-MER)
KeywordsTRANSFERASE/RNA / protein-rna complex / TRANSFERASE-RNA COMPLEX
Function / homology
Function and homology information


CCA tRNA nucleotidyltransferase / tRNA surveillance / CCACCA tRNA nucleotidyltransferase activity / CCA tRNA nucleotidyltransferase activity / tRNA 3'-terminal CCA addition / RNA repair / tRNA binding / magnesium ion binding / ATP binding
Similarity search - Function
CCA tRNA nucleotidyltransferase, domain 2 / Archaeal tRNA CCA-adding enzyme catalytic domain / tRNA nucleotidyltransferase, archaea / tRNA nucleotidyltransferase, substrate binding / tRNA nucleotidyltransferase, domain 2 / : / tRNA nucleotidyltransferase, second domain / CCA-adding enzyme, C-terminal domain / Poly(A) polymerase predicted RNA binding domain / Nucleotidyltransferase, class I-like, C-terminal ...CCA tRNA nucleotidyltransferase, domain 2 / Archaeal tRNA CCA-adding enzyme catalytic domain / tRNA nucleotidyltransferase, archaea / tRNA nucleotidyltransferase, substrate binding / tRNA nucleotidyltransferase, domain 2 / : / tRNA nucleotidyltransferase, second domain / CCA-adding enzyme, C-terminal domain / Poly(A) polymerase predicted RNA binding domain / Nucleotidyltransferase, class I-like, C-terminal / 2-5OAS/ClassI-CCAase, nucleotidyltransferase domain / Polymerase, nucleotidyl transferase domain / Poly(a)-polymerase, middle domain / Nucleotidyltransferase domain / Beta Polymerase, domain 2 / Beta Polymerase; domain 2 / Nucleotidyltransferase superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / CCA-adding enzyme
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsTomita, K. / Ishitani, R. / Fukai, S. / Nureki, O.
CitationJournal: Nature / Year: 2006
Title: Complete crystallographic analysis of the dynamics of CCA sequence addition
Authors: Tomita, K. / Ishitani, R. / Fukai, S. / Nureki, O.
History
DepositionJun 8, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 31, 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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: tRNA (32-MER)
A: CCA-adding enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,9554
Polymers61,7632
Non-polymers1922
Water1,856103
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.112, 58.112, 441.926
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: RNA chain tRNA (32-MER)


Mass: 10294.140 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Protein CCA-adding enzyme / tRNA nucleotidyltransferase / tRNA adenylyl-/cytidylyl- transferase / tRNA CCA-pyrophosphorylase / tRNA-NT


Mass: 51469.137 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Production host: Escherichia coli (E. coli) / References: UniProt: O28126, EC: 2.7.7.25, EC: 2.7.7.21
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 3.02 Å3/Da / Density % sol: 59.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: 50mM HEPES, 20% PEG 3550, 0.2M Tri-lithium citrate, 80mM NH4SO4, pH 7.5, VAPOR DIFFUSION, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1HEPES11
2PEG 355011
3Tri-lithium citrate11
4ammonium sulphate11
5water11
6HEPES12
7PEG 355012
8Tri-lithium citrate12
9ammonium sulphate12
10water12

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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: May 17, 2005
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 19376 / Num. obs: 19376 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 80 Å2
Reflection shellResolution: 2.8→2.9 Å / % possible all: 97.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UET

1uet


Resolution: 2.8→10 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 2888737.69 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.292 941 4.8 %RANDOM
Rwork0.236 ---
obs0.236 19376 99.4 %-
all-19376 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.280021 e/Å3
Displacement parametersBiso mean: 56.8 Å2
Baniso -1Baniso -2Baniso -3
1--8.3 Å20 Å20 Å2
2---8.3 Å20 Å2
3---16.61 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.45 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3630 684 10 103 4427
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d21
X-RAY DIFFRACTIONc_improper_angle_d1.07
X-RAY DIFFRACTIONc_mcbond_it1.271.5
X-RAY DIFFRACTIONc_mcangle_it2.172
X-RAY DIFFRACTIONc_scbond_it1.862
X-RAY DIFFRACTIONc_scangle_it2.932.5
LS refinement shellResolution: 2.8→2.97 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.375 1363 4.3 %
Rwork0.318 3035 -
obs--98.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramcarbohydrate.top
X-RAY DIFFRACTION5SO4.paramion.top

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