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- PDB-4x0a: Structure of tRNA-processing enzyme complex 6 -

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Basic information

Entry
Database: PDB / ID: 4x0a
TitleStructure of tRNA-processing enzyme complex 6
Components
  • Poly A polymerase
  • RNA (73-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
RNA / RNA (> 10) / A-adding tRNA nucleotidyltransferase
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
Thermotoga maritima MSB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.505 Å
AuthorsYamashita, S. / Tomita, K.
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
DepositionNov 21, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 15, 2015Provider: repository / Type: Initial release
Revision 1.1May 27, 2015Group: Database references
Revision 1.2Nov 20, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy
Category: citation / diffrn_source ...citation / diffrn_source / entity_src_gen / pdbx_entity_src_syn / pdbx_struct_oper_list / reflns_shell
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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 (73-MER)


Theoretical massNumber of molelcules
Total (without water)70,0562
Polymers70,0562
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)58.050, 110.300, 123.450
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


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) / Strain (production host): BL21(DE3) / References: UniProt: O66728
#2: RNA chain RNA (73-MER) / tRNAphe


Mass: 23504.965 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Thermotoga maritima MSB8 (bacteria)

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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: 2.82 Å3/Da / Density % sol: 56.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: isopropanol, potassium chloride, magnesium chloride, sodium cacodylate

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.5→20 Å / Num. obs: 10392 / % possible obs: 99.9 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 12
Reflection shellResolution: 3.5→3.63 Å / Redundancy: 6.3 % / Rmerge(I) obs: 1.614 / Mean I/σ(I) obs: 1.3 / Rejects: 0 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WC3

4wc3


Resolution: 3.505→19.742 Å / FOM work R set: 0.615 / SU ML: 0.65 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 41.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.312 518 5 %
Rwork0.2587 9837 -
obs0.2614 10355 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 899.91 Å2 / Biso mean: 325.49 Å2 / Biso min: 103.6 Å2
Refinement stepCycle: final / Resolution: 3.505→19.742 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3046 1557 0 0 4603
Num. residues----440
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024836
X-RAY DIFFRACTIONf_angle_d0.4676859
X-RAY DIFFRACTIONf_chiral_restr0.019827
X-RAY DIFFRACTIONf_plane_restr0.002590
X-RAY DIFFRACTIONf_dihedral_angle_d13.2592090
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.5-3.630.43851250.35882395252099
3.63-4.40770.33171280.27982412254099
4.4077-5.53290.32121290.269624552584100
5.5329-19.74270.28461360.231525752711100
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)
16.1128-3.236-1.12176.11622.18193.0069-1.1021-0.2848-1.17752.4955-0.12420.32551.4483-0.20220.32061.8571-0.0740.58411.22820.04271.946263.7866137.8723143.7211
210.41671.30371.52530.05920.4430.1716-0.8613-0.9272-1.36451.9662-0.78840.02851.85740.23031.00955.9720.49040.33462.31210.38242.740765.4645157.7769172.9195
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and resid 1:381A1 - 381
2X-RAY DIFFRACTION2chain B and resid 1:73B1 - 73

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