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- PDB-3ouy: How the CCA-adding Enzyme Selects Adenine Over Cytosine at Positi... -

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Basic information

Entry
Database: PDB / ID: 3ouy
TitleHow the CCA-adding Enzyme Selects Adenine Over Cytosine at Position 76 of tRNA
Components
  • (CCA-Adding Enzyme) x 2
  • RNA (35-MER)
KeywordsTransferase/RNA / Protein-RNA complex / Rossmann Fold / CCA-Adding / tRNA / Phospholation / Transferase-RNA complex
Function / homology
Function and homology information


CCACCA tRNA nucleotidyltransferase activity / CCA tRNA nucleotidyltransferase / tRNA 3'-terminal CCA addition / tRNA surveillance / 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
PYROPHOSPHATE 2- / RNA / RNA (> 10) / CCA-adding enzyme
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 Å
AuthorsPan, B.C. / Xiong, Y. / Steitz, T.A.
CitationJournal: Science / Year: 2010
Title: How the CCA-Adding Enzyme Selects Adenine over Cytosine at Position 76 of tRNA.
Authors: Pan, B. / Xiong, Y. / Steitz, T.A.
History
DepositionSep 15, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 1, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: CCA-Adding Enzyme
B: CCA-Adding Enzyme
C: RNA (35-MER)
D: RNA (35-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,41410
Polymers125,7124
Non-polymers7026
Water2,468137
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12700 Å2
ΔGint-94 kcal/mol
Surface area49160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.217, 228.075, 58.459
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein CCA-Adding Enzyme / tRNA nucleotidyltransferase / tRNA adenylyl-/cytidylyl- transferase / tRNA CCA-pyrophosphorylase / tRNA-NT


Mass: 51909.758 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Archaeoglobus fulgidus (archaea) / References: UniProt: O28126, EC: 2.7.7.25, EC: 2.7.7.21
#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 natural source / Source: (natural) Archaeoglobus fulgidus (archaea) / References: UniProt: O28126, EC: 2.7.7.25, EC: 2.7.7.21

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RNA chain , 1 types, 2 molecules CD

#3: RNA chain RNA (35-MER)


Mass: 11166.653 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: chemical synthesis

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Non-polymers , 4 types, 143 molecules

#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H2O7P2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 2.95 Å3/Da / Density % sol: 58.29 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG 4000, 0.2 M tri-lithium citrate, 80 mM ammonium sulfate, 50 mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 12, 2007
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.69→50 Å / Num. obs: 47752 / % possible obs: 91.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.2 % / Rsym value: 0.163 / Net I/σ(I): 13.8
Reflection shell
Resolution (Å)Rsym value% possible all
2.69-2.820.89186.5
2.82-2.960.70386.4
2.96-3.150.46687.1
3.15-3.390.30190.3
3.39-3.730.21895
3.73-4.270.17498.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.69→50 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.878 / SU B: 29.283 / SU ML: 0.287 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.353 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26374 1968 5 %RANDOM
Rwork0.20651 ---
obs0.20935 37297 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.43 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å20 Å20 Å2
2--0.17 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.69→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7284 1484 37 137 8942
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0229129
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4312.1812616
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8435876
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.24722.784388
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.489151396
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5161580
X-RAY DIFFRACTIONr_chiral_restr0.0920.21388
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026400
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2170.24170
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3110.26129
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2302
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1770.242
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2270.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4541.54474
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.8227068
X-RAY DIFFRACTIONr_scbond_it1.15635637
X-RAY DIFFRACTIONr_scangle_it1.9584.55548
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.69→2.76 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 143 -
Rwork0.321 2500 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.11550.66071.1782.27110.09241.50320.1373-0.0440.2153-0.0959-0.1038-0.0642-0.0777-0.0787-0.03350.0138-0.01530.0352-0.1386-0.0033-0.20954.549762.1061-8.4736
22.32310.1974-1.08722.44060.1063.340.01390.1270.0265-0.09940.03960.18010.0076-0.2676-0.0535-0.0317-0.0363-0.0507-0.16160.0254-0.144234.444847.3129-10.6038
33.04930.71560.10971.245-0.81972.44780.115-0.2840.23940.0669-0.06840.0802-0.28290.0323-0.04650.0235-0.03330.0195-0.1542-0.0417-0.183134.567845.230920.6864
42.141-1.0412-1.063310.0532-1.94391.1624-0.0108-0.414-0.67690.3223-0.3051-1.0338-0.1850.79540.3159-0.0379-0.0736-0.11550.12130.230.210738.544213.835734.7832
56.20920.61561.49584.2593-0.90863.61770.25540.1113-1.04090.0986-0.4128-0.18870.55990.31640.15740.04540.111-0.0353-0.54010.03610.288713.8631-24.913836.9408
65.24011.27521.05634.4086-0.17692.19160.1231-0.2103-0.8440.395-0.299-1.2830.33990.62820.1758-0.20430.178-0.0054-0.240.22160.366834.5493-10.484738.2461
74.20282.02140.30244.2177-0.74252.36290.1274-0.2226-0.15970.253-0.23830.28460.0099-0.10020.111-0.0401-0.09230.0324-0.2851-0.0038-0.122415.466614.12732.8671
82.07150.1148-1.19552.388-0.57677.8286-0.20420.3635-0.1556-0.13880.21440.43090.5665-0.5465-0.0102-0.0071-0.0416-0.0304-0.2360.0424-0.078721.115434.09445.9205
91.78671.241-1.31043.4427-4.08676.247-0.0123-0.2286-0.6543-0.5941-0.8389-0.73850.73841.20510.8513-0.02910.12880.06420.05260.15560.055954.619731.328713.6463
101.2062-0.10240.716911.4525-7.28474.9862-0.16750.464-0.2657-2.17610.2315-0.10531.52880.7023-0.0640.429-0.15740.05340.0547-0.0977-0.174516.49042.797610.7442
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A16 - 143
2X-RAY DIFFRACTION2A1 - 15
3X-RAY DIFFRACTION2A144 - 259
4X-RAY DIFFRACTION3A260 - 339
5X-RAY DIFFRACTION3A384 - 441
6X-RAY DIFFRACTION4A340 - 383
7X-RAY DIFFRACTION5B16 - 143
8X-RAY DIFFRACTION6B1 - 15
9X-RAY DIFFRACTION6B144 - 259
10X-RAY DIFFRACTION7B260 - 339
11X-RAY DIFFRACTION7B384 - 437
12X-RAY DIFFRACTION8B340 - 383
13X-RAY DIFFRACTION9C1 - 35
14X-RAY DIFFRACTION10D1 - 35

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