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- PDB-1sz1: Mechanism of CCA-adding enzymes specificity revealed by crystal s... -

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Basic information

Entry
Database: PDB / ID: 1sz1
TitleMechanism of CCA-adding enzymes specificity revealed by crystal structures of ternary complexes
Components
  • T-RNA (76-MER)
  • tRNA nucleotidyltransferase
KeywordsTRANSFERASE/RNA / CCA-adding enzyme / specificity / tRNA / complex / TRANSFERASE-RNA COMPLEX
Function / homology
Function and homology information


CCA tRNA nucleotidyltransferase / tRNA surveillance / CCACCA tRNA nucleotidyltransferase activity / tRNA 3'-terminal CCA addition / RNA repair / tRNA binding / magnesium ion binding / ATP binding
Similarity search - Function
tRNA nucleotidyltransferase, archaea / tRNA nucleotidyltransferase, substrate binding / tRNA nucleotidyltransferase, domain 2 / : / tRNA nucleotidyltransferase, second domain / CCA-adding enzyme, C-terminal domain / Nucleotidyltransferase, class I-like, C-terminal / 2-5OAS/ClassI-CCAase, nucleotidyltransferase domain / Polymerase, nucleotidyl transferase domain / Nucleotidyltransferase domain / Nucleotidyltransferase superfamily
Similarity search - Domain/homology
RNA / RNA (> 10) / CCA-adding enzyme
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 6.21 Å
AuthorsXiong, Y. / Steitz, T.A.
CitationJournal: Nature / Year: 2004
Title: Mechanism of transfer RNA maturation by CCA-adding enzyme without using an oligonucleotide template.
Authors: Xiong, Y. / Steitz, T.A.
History
DepositionApr 2, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Aug 23, 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_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: T-RNA (76-MER)
F: T-RNA (76-MER)
A: tRNA nucleotidyltransferase
B: tRNA nucleotidyltransferase


Theoretical massNumber of molelcules
Total (without water)152,7194
Polymers152,7194
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)218.403, 218.403, 170.263
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12E
22F

NCS domain segments:

Component-ID: 1 / Refine code: 2

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETASPASPAC1 - 4371 - 437
21METMETASPASPBD1 - 4371 - 437
12GGAAEA1 - 761 - 76
22GGAAFB1 - 761 - 76

NCS ensembles :
ID
1
2

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Components

#1: RNA chain T-RNA (76-MER)


Mass: 24890.121 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein tRNA nucleotidyltransferase / 2.7.7.25 / tRNA adenylyltransferase / tRNA CCA-pyrophosphorylase / CCA-adding enzyme


Mass: 51469.137 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: O28126, EC: 2.7.7.25

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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 % sol: 84 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: (NH4)2SO4, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1(NH4)2SO411
2H2O11
3(NH4)2SO412
4H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 6.21→50 Å / Num. obs: 10111 / Rmerge(I) obs: 0.102 / Rsym value: 0.102 / Net I/σ(I): 12.2
Reflection shellHighest resolution: 6.21 Å / Mean I/σ(I) obs: 1.5 / % possible all: 97.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1R89

1r89


Resolution: 6.21→44.72 Å / Cor.coef. Fo:Fc: 0.715 / Cor.coef. Fo:Fc free: 0.74 / Cross valid method: THROUGHOUT / ESU R Free: 2.455 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.37962 574 5.4 %RANDOM
Rwork0.36023 ---
obs0.36131 10111 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 101.709 Å2
Baniso -1Baniso -2Baniso -3
1--0.48 Å2-0.24 Å20 Å2
2---0.48 Å20 Å2
3---0.73 Å2
Refinement stepCycle: LAST / Resolution: 6.21→44.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7260 3296 0 0 10556
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02211108
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3782.34415706
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9695872
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.18822.784388
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.385151390
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0021580
X-RAY DIFFRACTIONr_chiral_restr0.1290.21794
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.027286
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2210.25116
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.27346
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2325
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3210.257
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2090.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.0072.54352
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.01547028
X-RAY DIFFRACTIONr_scbond_it0.77356756
X-RAY DIFFRACTIONr_scangle_it0.84788678
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1748tight positional0.010.05
1A1882medium positional0.020.5
2B1648medium positional0.090.5
1A1748tight thermal00.5
1A1882medium thermal0.022
2B1648medium thermal0.062
LS refinement shellResolution: 6.214→6.634 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.418 96 -
Rwork0.401 1724 -
obs--100 %

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