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- PDB-1ou5: Crystal structure of human CCA-adding enzyme -

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Basic information

Entry
Database: PDB / ID: 1ou5
TitleCrystal structure of human CCA-adding enzyme
ComponentstRNA CCA-adding enzyme
KeywordsTRANSLATION / TRANSFERASE / tRNA / polymerase / nucleotidyltransferase
Function / homology
Function and homology information


5'-3' RNA polymerase activity / CCA tRNA nucleotidyltransferase activity / tRNA processing in the mitochondrion / mitochondrial tRNA 3'-end processing / tRNA surveillance / CCACCA tRNA nucleotidyltransferase activity / CCA tRNA nucleotidyltransferase / tRNA 3'-end processing / tRNA 3'-terminal CCA addition / tRNA processing in the nucleus ...5'-3' RNA polymerase activity / CCA tRNA nucleotidyltransferase activity / tRNA processing in the mitochondrion / mitochondrial tRNA 3'-end processing / tRNA surveillance / CCACCA tRNA nucleotidyltransferase activity / CCA tRNA nucleotidyltransferase / tRNA 3'-end processing / tRNA 3'-terminal CCA addition / tRNA processing in the nucleus / rescue of stalled ribosome / tRNA binding / mitochondrial matrix / protein homodimerization activity / mitochondrion / nucleoplasm / ATP binding / nucleus / metal ion binding / cytosol
Similarity search - Function
cca-adding enzyme, domain 2 / cca-adding enzyme, domain 2 / tRNA nucleotidyltransferase/poly(A) polymerase, RNA and SrmB- binding domain / Probable RNA and SrmB- binding site of polymerase A / Poly A polymerase, head domain / Poly A polymerase head domain / Beta Polymerase, domain 2 / Beta Polymerase; domain 2 / Nucleotidyltransferase superfamily / 2-Layer Sandwich ...cca-adding enzyme, domain 2 / cca-adding enzyme, domain 2 / tRNA nucleotidyltransferase/poly(A) polymerase, RNA and SrmB- binding domain / Probable RNA and SrmB- binding site of polymerase A / Poly A polymerase, head domain / Poly A polymerase head domain / Beta Polymerase, domain 2 / Beta Polymerase; domain 2 / Nucleotidyltransferase superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
CCA tRNA nucleotidyltransferase 1, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SIR / Resolution: 3.4 Å
AuthorsAugustin, M.A. / Reichert, A.S. / Betat, H. / Huber, R. / Moerl, M. / Steegborn, C.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Crystal Structure of the Human CCA-adding Enzyme: Insights into Template-independent Polymerization
Authors: Augustin, M.A. / Reichert, A.S. / Betat, H. / Huber, R. / Moerl, M. / Steegborn, C.
History
DepositionMar 24, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Advisory / Refinement description
Category: pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / refine_ls_shell
Item: _refine_ls_shell.percent_reflns_obs

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: tRNA CCA-adding enzyme
B: tRNA CCA-adding enzyme


Theoretical massNumber of molelcules
Total (without water)102,4502
Polymers102,4502
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area880 Å2
ΔGint-9 kcal/mol
Surface area35120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.520, 102.520, 206.658
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Cell settingtrigonal
Space group name H-MP3221

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Components

#1: Protein tRNA CCA-adding enzyme / CCA-adding enzyme / tRNA-nucleotidyltransferase / CGI-47 protein


Mass: 51225.145 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: hMtCCA / Plasmid: PET30EK-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RP / References: UniProt: Q96Q11

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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: 4.02 Å3/Da / Density % sol: 69.2 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 100mM sodium citrate, 2.2M ammonium sulfate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mMTris-HCl1droppH7.5
2400 mM1dropNaCl
30.02 %(w/v)1dropNaN3
42 mMdithiothreitol1drop
56 mg/mlprotein1drop
6100 mMsodium citrate1reservoirpH5.6
72.2 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 21, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.4→50 Å / Num. obs: 17609 / % possible obs: 98.9 % / Observed criterion σ(I): 1 / Redundancy: 2.7 % / Biso Wilson estimate: 78.9 Å2 / Rmerge(I) obs: 0.076 / Rsym value: 0.076 / Net I/σ(I): 9
Reflection shellResolution: 3.4→3.58 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.373 / Mean I/σ(I) obs: 2.1 / Num. unique all: 2373 / Rsym value: 0.373 / % possible all: 98.9
Reflection
*PLUS
Lowest resolution: 25 Å / Num. obs: 17538 / % possible obs: 99.1 % / Num. measured all: 46729 / Rmerge(I) obs: 0.069
Reflection shell
*PLUS
% possible obs: 98.9 % / Rmerge(I) obs: 0.273 / Mean I/σ(I) obs: 2.7

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
REFMAC5refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: SIR / Resolution: 3.4→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.318 1742 10 %RANDOM
Rwork0.278 ---
all0.282 17859 --
obs0.282 17538 98.2 %-
Refinement stepCycle: LAST / Resolution: 3.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5570 0 0 0 5570
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.012
X-RAY DIFFRACTIONr_bond_other_d0.002
X-RAY DIFFRACTIONr_angle_refined_deg1.77
X-RAY DIFFRACTIONr_angle_other_deg1.13
LS refinement shellResolution: 3.4→3.486 Å
RfactorNum. reflection
Rfree0.399 114
Rwork0.36 -
obs-1149
Refinement
*PLUS
Highest resolution: 3.4 Å / Lowest resolution: 20 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg1.6

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