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- PDB-4wby: tRNA-processing enzyme (apo form I) -

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Basic information

Entry
Database: PDB / ID: 4wby
TitletRNA-processing enzyme (apo form I)
ComponentsPoly A polymerase
KeywordsTRANSFERASE / RNA Nucleotidyltransferase / CCA-adding enzyme / A-adding enzyme
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
A-adding tRNA nucleotidyltransferase
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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_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_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 / diffrn_radiation_wavelength / 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.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Poly A polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8027
Polymers48,2301
Non-polymers5726
Water8,791488
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area920 Å2
ΔGint-45 kcal/mol
Surface area20140 Å2
Unit cell
Length a, b, c (Å)54.510, 67.740, 127.500
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 48229.617 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 428-824
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: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 488 / Source method: isolated from a natural source / Formula: H2O

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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: 2.44 Å3/Da / Density % sol: 49.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG3350, potassium sulfate

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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: May 18, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 75966 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 9.5 % / Biso Wilson estimate: 18.66 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.04 / Rrim(I) all: 0.043 / Χ2: 0.992 / Net I/σ(I): 30.42 / Num. measured all: 719782
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
1.5-1.540.9530.3826.1351795556055260.40499.4
1.54-1.580.9720.3077.7652829541954160.32499.9
1.58-1.630.9790.2499.4751563527552750.262100
1.63-1.680.9870.19911.750444515751560.21100
1.68-1.730.9920.15914.2648989499549950.167100
1.73-1.790.9950.12517.7447272481948190.131100
1.79-1.860.9970.10121.3445802467246720.107100
1.86-1.940.9980.0826.0944128451045100.085100
1.94-2.020.9980.06431.7441965432443240.067100
2.02-2.120.9990.05138.1639906412641260.053100
2.12-2.240.9990.04442.9237751394439440.046100
2.24-2.370.9990.03947.6635386373537350.041100
2.37-2.540.9990.03650.6933078350835070.038100
2.54-2.740.9990.03354.0430507329132910.035100
2.74-30.9990.03256.3627899304730470.034100
3-3.350.9990.0359.6824969276027600.032100
3.35-3.870.9990.02962.0121114244924390.0399.6
3.87-4.740.9990.02860.916304209820350.0397
4.74-6.710.9990.0361.1313155166716370.03298.2
6.710.9980.03154.5949269697520.03477.6

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Processing

Software
NameVersionClassification
XDSdata reduction
PHENIX(phenix.refine: 1.8.4_1496)refinement
PDB_EXTRACT3.15data extraction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VFG

1vfg


Resolution: 1.5→19.94 Å / FOM work R set: 0.9156 / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 14.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1761 3797 5 %
Rwork0.1558 72144 -
obs0.1568 75941 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 72.54 Å2 / Biso mean: 28.97 Å2 / Biso min: 10.64 Å2
Refinement stepCycle: final / Resolution: 1.5→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3085 0 31 488 3604
Biso mean--35.75 39.2 -
Num. residues----372
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053182
X-RAY DIFFRACTIONf_angle_d0.9584267
X-RAY DIFFRACTIONf_chiral_restr0.037473
X-RAY DIFFRACTIONf_plane_restr0.005526
X-RAY DIFFRACTIONf_dihedral_angle_d11.9811242
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.5190.22091350.15052564269999
1.519-1.5390.17351410.138826802821100
1.539-1.56010.17041400.125426552795100
1.5601-1.58230.17461380.123826172755100
1.5823-1.60590.15961410.123926832824100
1.6059-1.6310.18871380.120126212759100
1.631-1.65780.15961410.116826832824100
1.6578-1.68630.15531380.119126202758100
1.6863-1.7170.19961400.126226652805100
1.717-1.750.16681410.124726652806100
1.75-1.78570.16741390.128526572796100
1.7857-1.82450.1841430.132627022845100
1.8245-1.86690.15611380.130426292767100
1.8669-1.91350.19141390.135726482787100
1.9135-1.96520.18371420.135426932835100
1.9652-2.0230.16621410.138826822823100
2.023-2.08820.15181410.137426662807100
2.0882-2.16280.17891400.136226752815100
2.1628-2.24930.15971420.138426932835100
2.2493-2.35150.16181420.136226952837100
2.3515-2.47530.17261420.147126972839100
2.4753-2.630.16791420.157126982840100
2.63-2.83260.17761420.167627072849100
2.8326-3.11660.16321440.17327182862100
3.1166-3.56540.21591440.164827472891100
3.5654-4.48360.161430.16182707285098
4.4836-19.94210.19661400.21362677281792

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