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- PDB-4wc2: Crystal structure of tRNA nucleotidyltransferase complexed with a... -

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Basic information

Entry
Database: PDB / ID: 4wc2
TitleCrystal structure of tRNA nucleotidyltransferase complexed with a primer tRNA and an incoming ATP analog
Components
  • Poly A polymerase
  • RNA 75-mer
KeywordsTRANSFERASE/RNA / RNA Nucleotidyltransferase / CCA-adding enzyme / A-adding enzyme / TRANSFERASE-RNA complex
Function / homology
Function and homology information


ATP:3'-cytidine-cytidine-tRNA adenylyltransferase activity / tRNA processing / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / tRNA binding / ATP binding / metal ion binding
Similarity search - Function
: / cca-adding enzyme, domain 2 / cca-adding enzyme, domain 2 / Poly A polymerase, head domain / Poly A polymerase head domain / DHH phosphoesterase superfamily / DHHA1 domain / DHHA1 domain / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily ...: / cca-adding enzyme, domain 2 / cca-adding enzyme, domain 2 / Poly A polymerase, head domain / Poly A polymerase head domain / DHH phosphoesterase superfamily / DHHA1 domain / DHHA1 domain / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile. / Beta Polymerase, domain 2 / Beta Polymerase; domain 2 / Nucleotidyltransferase superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / : / RNA / RNA (> 10) / A-adding tRNA nucleotidyltransferase
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
Thermotoga maritima MSB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å
AuthorsYamashita, S. / Tomita, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Science and Technology Agency (JST)LS135 Japan
CitationJournal: Structure / Year: 2015
Title: Measurement of Acceptor-T Psi C Helix Length of tRNA for Terminal A76-Addition by A-Adding Enzyme.
Authors: Yamashita, S. / Martinez, A. / Tomita, K.
History
DepositionSep 4, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 15, 2015Provider: repository / Type: Initial release
Revision 1.1May 27, 2015Group: Database references
Revision 1.2Sep 27, 2017Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Source and taxonomy
Category: citation / diffrn_detector ...citation / diffrn_detector / diffrn_source / entity_src_gen / pdbx_database_status / pdbx_entity_src_syn / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_detector.detector ..._citation.journal_id_CSD / _diffrn_detector.detector / _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein
Revision 1.4Mar 19, 2025Group: Database references / Structure summary / Category: pdbx_database_related / pdbx_entry_details / Item: _pdbx_database_related.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Poly A polymerase
B: RNA 75-mer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,2364
Polymers70,7062
Non-polymers5302
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3020 Å2
ΔGint-14 kcal/mol
Surface area30690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.920, 109.480, 125.900
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Poly A polymerase / A-adding enzyme


Mass: 46550.711 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 443-824
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Gene: pcnB1, aq_411 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / References: UniProt: O66728
#2: RNA chain RNA 75-mer


Mass: 24155.350 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: tRNAphe from Thermotoga maritima / Source: (synth.) Thermotoga maritima MSB8 (bacteria) / References: GenBank: 12057205
#3: Chemical ChemComp-APC / DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-CPP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
Has protein modificationN

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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: 2.87 Å3/Da / Density % sol: 57.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: MPD, magnesium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Dec 9, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 20480 / % possible obs: 99.2 % / Redundancy: 6.2 % / Biso Wilson estimate: 72.5 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 22.4
Reflection shellResolution: 2.8→2.87 Å / Rmerge(I) obs: 0.398 / Mean I/σ(I) obs: 4.3 / % possible all: 95.7

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
PDB_EXTRACT3.15data extraction
RefinementResolution: 2.8→19.802 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.76 / Phase error: 25.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2672 1024 5 %
Rwork0.2154 19456 -
obs0.218 20480 99.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 446.84 Å2 / Biso mean: 169.4754 Å2 / Biso min: 35.92 Å2
Refinement stepCycle: final / Resolution: 2.8→19.802 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3046 1601 32 0 4679
Biso mean--107.7 --
Num. residues----442
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024918
X-RAY DIFFRACTIONf_angle_d0.6156989
X-RAY DIFFRACTIONf_chiral_restr0.021841
X-RAY DIFFRACTIONf_plane_restr0.003593
X-RAY DIFFRACTIONf_dihedral_angle_d14.7532130
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8-2.94720.30141390.25692654279396
2.9472-3.13120.32741430.24372713285699
3.1312-3.37180.24261450.207827522897100
3.3718-3.70910.23491470.200627962943100
3.7091-4.24130.25821460.189827902936100
4.2413-5.32630.24231480.200128172965100
5.3263-19.80260.29071560.23522934309099
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)
12.0911-0.74210.06074.43220.0921.596-0.1794-0.4304-0.24921.41960.02450.21460.2901-0.1510.09930.7859-0.03950.16220.50710.02550.664564.9883137.0343146.7516
22.8268-0.4745-0.24981.62092.38773.4286-1.3783-1.1978-0.55822.37640.5608-0.18550.27310.83770.82594.89980.33720.17711.81540.0361.588366.5325156.4072177.6459
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 1:381)A1 - 381
2X-RAY DIFFRACTION2(chain B and resid 1:75)B1 - 75

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