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- PDB-4wc4: tRNA-processing enzyme complex 2 -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 4wc4
TitletRNA-processing enzyme complex 2
Components
  • Poly A polymerase
  • RNA (74-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
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 / Resolution: 3.501 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 1.3Mar 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

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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 (74-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,9083
Polymers70,4012
Non-polymers5071
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.310, 111.760, 127.990
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 (74-MER)


Mass: 23850.168 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


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: 3.01 Å3/Da / Density % sol: 59.17 %
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: 3.5→20 Å / Num. obs: 11158 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 95.74 Å2 / Rmerge F obs: 0.995 / Rmerge(I) obs: 0.222 / Rrim(I) all: 0.239 / Χ2: 0.969 / Net I/σ(I): 8.94 / Num. measured all: 80315
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
3.5-3.590.7621.3091.8657748027971.4199.4
3.59-3.690.8261.1042.3358827927911.18799.9
3.69-3.80.9380.932.6756817707701100
3.8-3.910.9060.7563.3556477617610.812100
3.91-4.040.9450.6064.0953167247240.652100
4.04-4.190.9780.4345.3752177057040.46799.9
4.19-4.340.970.3836.0449356716710.412100
4.34-4.520.9840.3087.3249966846840.332100
4.52-4.720.9840.2488.4845406226220.267100
4.72-4.950.9910.2049.6644286116110.219100
4.95-5.220.9870.2269.541165645640.244100
5.22-5.540.9850.2239.6740215565560.24100
5.54-5.920.9880.2049.8738315345340.22100
5.92-6.390.990.18710.8634244814810.201100
6.39-70.990.15113.132104544540.163100
7-7.830.9970.09218.2728594134130.099100
7.83-9.040.9970.06425.6324653723720.07100
9.04-11.070.9980.04730.9119943153140.05199.7
11.07-15.660.9970.04332.915632652610.04798.5
15.660.9980.03931.27416156740.04347.4

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Processing

Software
NameVersionClassification
XDSdata reduction
PHENIX(phenix.refine: 1.9_1692)refinement
PDB_EXTRACT3.15data extraction
XSCALEdata scaling
RefinementResolution: 3.501→19.881 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 37.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.302 557 5 %
Rwork0.2769 10582 -
obs0.2782 11139 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 494.39 Å2 / Biso mean: 224.6063 Å2 / Biso min: 68.05 Å2
Refinement stepCycle: final / Resolution: 3.501→19.881 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3046 1581 31 0 4658
Biso mean--151.38 --
Num. residues----441
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024896
X-RAY DIFFRACTIONf_angle_d0.4926955
X-RAY DIFFRACTIONf_chiral_restr0.019836
X-RAY DIFFRACTIONf_plane_restr0.002592
X-RAY DIFFRACTIONf_dihedral_angle_d14.3562115
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
3.5014-3.590.36021350.329725782713
3.59-4.40350.27161370.281726062743
4.4035-5.52810.32641390.285126292768
5.5281-19.88130.28541460.253527692915
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)
12.6963-0.4758-0.0523.74081.41670.5419-0.2476-0.5224-0.7571.9496-0.3680.06690.6302-0.19610.52311.0239-0.15270.27160.6720.13882.085765.9696140.0883148.4889
24.2476-0.12710.17190.22390.78742.8625-0.8161-0.6597-0.87331.55260.08120.63610.35450.09350.74635.13680.25810.15081.75280.08272.444467.056159.9677179.8538
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 1:74)B1 - 74

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