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- PDB-4x0b: Structure of tRNA-processing enzyme complex 7 -

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Basic information

Entry
Database: PDB / ID: 4x0b
TitleStructure of tRNA-processing enzyme complex 7
Components
  • Poly A polymerase
  • RNA (77-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 / RNA 3'-end processing / 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 / CBS domain superfamily / Domain in cystathionine beta-synthase and other proteins. / CBS domain ...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 / CBS domain superfamily / Domain in cystathionine beta-synthase and other proteins. / 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: 3.2 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
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 / 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 / _reflns.pdbx_Rsym_value
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 (77-MER)


Theoretical massNumber of molelcules
Total (without water)71,3562
Polymers71,3562
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-12 kcal/mol
Surface area30970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.740, 110.070, 127.760
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
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 (77-MER) / tRNAphe


Mass: 24805.738 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: 2.89 Å3/Da / Density % sol: 57.5 %
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: 3.2→20 Å / Num. obs: 14222 / % possible obs: 99.9 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.163 / Rsym value: 0.151 / Net I/σ(I): 11.8
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 1.4 / Rsym value: 1.752 / Rejects: 0 / % possible all: 99.1

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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: 3.2→19.859 Å / FOM work R set: 0.6255 / SU ML: 0.61 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 39.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3036 708 5.01 %
Rwork0.2674 13436 -
obs0.2693 14144 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 577.92 Å2 / Biso mean: 230.77 Å2 / Biso min: 77.67 Å2
Refinement stepCycle: final / Resolution: 3.2→19.859 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3046 1643 0 0 4689
Num. residues----444
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024932
X-RAY DIFFRACTIONf_angle_d0.5217009
X-RAY DIFFRACTIONf_chiral_restr0.021847
X-RAY DIFFRACTIONf_plane_restr0.003594
X-RAY DIFFRACTIONf_dihedral_angle_d14.7382138
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2001-3.44610.47011390.3952624276399
3.4461-3.79070.33831370.327826272764100
3.7907-4.33420.33291410.263626612802100
4.3342-5.4420.26191420.245227112853100
5.442-19.85910.27671490.240628132962100
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)
14.1446-1.14340.08673.68411.03342.2237-0.3883-0.2201-0.32072.2664-0.0463-0.12790.4471-0.04530.47291.0753-0.11040.240.70110.08561.99964.852137.7847148.5318
22.932-0.2079-1.32160.16280.59041.9191-1.1554-0.8422-1.1252.61150.23180.42480.54410.22291.21145.24350.2649-0.02851.7688-0.02442.544467.1554157.2788177.9957
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 1:77B1 - 77

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