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- PDB-4wc6: Structure of tRNA-processing enzyme complex 4 -

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Basic information

Entry
Database: PDB / ID: 4wc6
TitleStructure of tRNA-processing enzyme complex 4
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 / 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
ADENOSINE-5'-TRIPHOSPHATE / : / 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: 3.41 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 1.2Jan 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Source and taxonomy
Category: citation / diffrn_source ...citation / diffrn_source / entity_src_gen / pdbx_database_status / pdbx_entity_src_syn / pdbx_struct_oper_list
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_database_status.pdb_format_compatible / _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 / 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

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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)71,2133
Polymers70,7062
Non-polymers5071
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2880 Å2
ΔGint-5 kcal/mol
Surface area30960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.220, 111.740, 127.800
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-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM

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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: 2.99 Å3/Da / Density % sol: 58.86 %
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: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.41→20 Å / Num. obs: 12086 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 14.6 % / Biso Wilson estimate: 103.76 Å2 / Rmerge F obs: 0.998 / Rmerge(I) obs: 0.207 / Rrim(I) all: 0.215 / Χ2: 1.019 / Net I/σ(I): 11.84 / Num. measured all: 172906
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
3.41-3.490.6692.0561.77127348848832.13199.9
3.49-3.590.8561.3052.76126038498491.352100
3.59-3.690.9281.013.4124648468461.047100
3.69-3.810.9660.8473.97116777997990.878100
3.81-3.930.9530.6664.93117607997990.69100
3.93-4.070.9840.4876.16110787567560.505100
4.07-4.220.9930.3448109947567560.357100
4.22-4.40.9930.2969.42101687007000.306100
4.4-4.590.9950.24311.45100446956950.252100
4.59-4.820.9970.18613.6593876466460.193100
4.82-5.080.9960.17814.3190626346340.184100
5.08-5.380.9950.17615.2686466026020.183100
5.38-5.760.9940.20513.7478715485480.213100
5.76-6.220.9960.16915.9475145355350.175100
6.22-6.810.9960.14219.1668404874870.148100
6.81-7.610.9980.09824.560964434430.102100
7.61-8.790.9980.07531.9953964034030.078100
8.79-10.770.9990.05839.2844753473470.06100
10.77-15.230.9980.05140.2932052762690.05397.5
15.230.9960.05136.3892174890.05451.1

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Processing

Software
NameVersionClassification
XDSdata reduction
PHENIX(phenix.refine: 1.9_1692)refinement
PDB_EXTRACT3.15data extraction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WC2

4wc2


Resolution: 3.41→19.872 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 38.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3273 605 5.01 %
Rwork0.267 11466 -
obs0.27 12071 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 561.17 Å2 / Biso mean: 242.7283 Å2 / Biso min: 80.18 Å2
Refinement stepCycle: final / Resolution: 3.41→19.872 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3046 1601 31 0 4678
Biso mean--189.96 --
Num. residues----442
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024918
X-RAY DIFFRACTIONf_angle_d0.5076989
X-RAY DIFFRACTIONf_chiral_restr0.02841
X-RAY DIFFRACTIONf_plane_restr0.002593
X-RAY DIFFRACTIONf_dihedral_angle_d14.1742127
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.4052-3.490.41531480.328928092957
3.7458-4.28310.30941490.277228242973
4.2831-5.37850.32281510.268328583009
5.3785-19.87230.31371570.245929753132
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)
14.3083-0.98780.04372.64491.5861.0625-0.4461-0.484-0.52352.6225-0.3674-0.31040.5221-0.03950.75481.3904-0.18590.42630.75170.14742.197565.8357140.0764148.321
24.1661-0.0133-1.0436-0.0070.01080.2597-1.7548-0.7408-1.00192.1784-0.02750.72580.47760.15771.79755.1920.1260.0861.81790.09672.475167.2637159.7404179.2269
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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